A dragonfly flies over a road in the desert. It dodges a semi and some cars traveling down the road. Its luck runs out when it runs into the windshield of a van. The driver curses bugs and turns on the wipers to remove it. Several Hispanics are crowded into the back of the van. The van approaches a row of spotlights, and then the driver tells his passengers (in Spanish) to be quiet. It is a U.S. Border Patrol ambush. INS Agent Janus (Fredric Lehne) asks the driver, "Nick the Slick" (Jon Gries) where he's going and he replies, "Fishin' in Cuernavaca." They go to the back of the van to look at his "catch". Janus orders all the Hispanics (in Spanish) to get out and form a line. He then asks Nick how much he got for each illegal alien, and then says that he should save it for his lawyer. A black car drives up and two men get out dressed in black suits. The driver, Agent K, "Kay", (Tommy Lee Jones) identifies themselves as INS Division 6, which Janus never heard of. Kay asks his partner, Agent D, "Dee", (Richard Hamilton), whom he's got his money on, and he says that it's a tough call. Kay walks up to each illegal and cordially asks them questions (in Spanish) such as "How are you?", "Going to Nogales?", and "Looking for work?". He also tells them not to worry and welcomes them to the United States. When he reaches the last illegal, Kay confronts him, telling him (in Spanish) that he'll break his face and that he's very ugly, but the man just nods and grunts in agreement. Satisfied that the man doesn't speak any Spanish, Kay tells Dee that they have a winner, and tells the other illegals (in Spanish) that they can go. Janus tries to stop them, but Kay tells him that he doesn't know whom he's dealing with. The van drives away with all the illegals inside, except their "winner", and then Kay tells the INS agents to leave.
Kay and Dee take the man away from the road and Kay tells the INS agents to keep protecting them from dangerous aliens. Another INS agent tells Janus that there is no Division 6. Kay bets the man that he's not from anywhere near there, and pulls out a switchblade. He cuts open the front of the man, revealing "Mikey", an extraterrestrial alien holding a fake human head. The alien roars and then speaks in his own language. Kay asks Mikey when they released him from jail. The alien complains, and Kay translates that he's a political refugee. Dee tells Mikey that he just violated seven treaties. Kay takes the head from Mikey, and then makes him raise his arms and flippers. Janus looks down from a hill and sees Mikey and then gasps. Mikey roars, pushes Dee down, and then charges at Janus. Kay tells Dee to shoot him, but Dee just fumbles with his gun. Like a deer frozen in car headlights, Janus stands petrified and screams even as Mikey leaps at him. Kay pulls out his gun and blasts Mikey dead, spraying blue guts all over Janus. Janus walks over to Kay and Dee in shock, stuttering as he tries to speak. The other INS agents rush over, and Kay assures them that everything is under control. A large black panel van pulls up. Several agents from a containment squad get out, holding flamethrowers and dressed in protective vinyl. Kay instructs them to perform a splay burn of the region to cover up any evidence of extraterrestrials. He then draws the INS agents' attention to a small device with a red strobe light; he says that it's a neuralizer, a gift from "some friends out of town", and that it will isolate memory impulses in their brains. As the INS agents lean forward for a better look, Janus asks Kay who he really is, and he tells them that he's just a figment of their imagination. Kay puts on his sunglasses and neuralizes the agents. He removes his sunglasses, and then tells the INS agents that they're lucky to be alive after that blast. Janus wonders what blast, and Kay claims that Janus discharged his gun and caused a gas main to explode.
Kay walks over to Dee, who sits sullenly. Dee says that it didn't use to happen. He looks up at the stars and says that they're beautiful. Accepting his imminent retirement, he tells Kay that he'll miss the chase. Kay puts on his sunglasses, sets the neuralizer to 1961, and replies, "No Dee, you won't", and then flashes the neuralizer.
James Edwards (Will Smith), an undercover NYPD officer, runs after a suspect/perp (Keith Campbell) in the night. Two uniformed officers, very overweight, quit running with Edwards and "let" him continue the chase alone. The suspect jumps off a bridge about 20 feet high to the street below, and then continues running. Edwards is surprised at the man's agility, but he doesn't give up; he jumps onto a passing double-decker tourist bus, then runs out and onto the back of a New York Post delivery van. When the van catches up to the suspect, Edwards jumps out and slams him into a wall. The suspect says, "He's coming! He's coming!", and then tries to shoot Edwards with an electronic weapon. Edwards knocks it to the ground and it vaporizes. The suspect takes off down the street again. They reach the Guggenheim Museum, and the suspect jumps about 15 feet onto the top of a wall, and then scales the side of a tall building onto the roof. Edwards shoots out the glass doors of the building entrance and then runs up a ramp. The suspect tries to open doors to leave the roof, finally finding one unlocked -- but finds Edwards there with his gun drawn. As the suspect backs up, he says, "He's coming. He's coming because I failed, and he'll kill me too," then tells Edwards that his world is going to end. He blinks his corneas sideways like shutters. Edwards asks him, "What the hell are you?" The suspect backs up against the edge of the roof. Edwards asks him to come back from the ledge, that they will get his eyes fixed. The suspect throws himself off the roof, landing with a thud on the ground below and dying.
At a bucolic farm in upstate New York, everything is peaceful except for the meteor that streaks towards it. Inside the house a man, Edgar (Vincent D'Onofrio), is complaining to his wife Beatrice (Siobhan Fallon Hogan) that when he gets home from work he wants a clean house and a fat steak. He calls the dinner poison, but complains when his wife takes it away. He calls Beatrice useless, and then tells her, "The only that pulls its weight around here is my goddamn truck." The meteor hits his pickup truck, obliterating it and setting a tree on fire. Edgar goes outside with his rifle to the meteor crater, and then an alien voice tells him to place his "projectile weapon" on the ground, Edgar replies, "You can have my gun after you pry it from my cold, dead fingers." The alien accepts his proposal, and then pulls him screaming into the crater with its large insectoid claw. The alien eats him, and then climbs out of the crater wearing Edgar's skin and skull like a suit. "Edgar" staggers back into the house with the rifle. Beatrice asks him what that was, but he just asks for sugar. She puts a spoonful of sugar into a glass of water, but he asks for more sugar until she pours the whole bowl of sugar into the glass; he downs it and sighs contentedly. She tells him that his skin is hanging off his bones. He looks at the mirror, and agrees. He pulls back his scalp, tightening the skin on his face, and shows it to her; she faints. "Edgar" goes back outside and rolls his flying saucer out of the crater.
Back at the police station, the police inspector and a cop who was with Edwards during the chase are questioning him about his report on the dead perp. They can't believe that the perpetrator blinked two sets of eyelids. Edwards says that it was after the weapon "evaporated into a million pieces." The officer asks him why no other officer saw these events, and Edwards replies that they are "a little soggy around the midsection and couldn't keep up." Edwards and the cop then argue, so the inspector takes the cop out of the room to talk. Laurel Weaver (Linda Fiorentino), Deputy Medical Examiner, comes in and tells Edwards that she believes him. She tells him to find her at the morgue on 26th and then leaves. We see Kay zap her with the neuralizer in the hallway then comes into the room. He unplugs the camera and then tells Edwards that those were gills, not eyes; the suspect was out of breath. Edwards asks Kay who he is. He doesn't answer, but instead asks Edwards if the suspect said anything. Edwards replies that he said the world was coming to an end. Kay asks if he said when, but Edwards just stares at him. Kay asks if he would recognize his weapon, and Edwards says, "Absolutely." Kay takes Edwards out of the room for "a ride", but he complains about the paperwork he has to complete. Kay tells him that its done. When Kay opens the door, the inspector comes by holding some paperwork and congratulates Edwards on "running down the dude on foot."
Kay drives Edwards while explaining that he's part of a bureau that licenses, monitors, and polices alien activity on the planet Earth; Edwards scoffs. They arrive at a pawnshop owned by Jack Jeebs, who Edwards says doesn't even sell guns. Edwards tells Kay to wait while he goes inside. Inside the shop, Jeebs (Tony Shalhoub) is examining some stolen Rolex watches on the counter, and jokes to Edwards about returning them. Edwards tells Jeebs that he's into something hotter than them, then asks him about unusual guns. Kay comes inside, holding his gun and tells Jeebs to show Edwards the imports. Jeebs claims he got out of that business. Kay tells him that he hates it when he lies, then points his gun at Jeebs and counts to three. On three, Kay shoots Jeebs, causing his head to blow off. Edwards points his own gun at Kay and orders him to drop his weapon and put his hands on his head, when suddenly Jeebs stands up, having grown a new head! He presses a button hidden under the counter and then several panels swing open, revealing alien weapons. Edwards identifies the weapon the perp pulled on him. Kay rebukes Jeebs for selling "a reverberating carbonizer with mutating capacity to an unlicensed cephalopoid." Kay says that it must have been for assassination, and asks Jeebs who's the target. Kay points his gun at Jeebs, who then says in desperation that he doesn't know. Kay tells Jeebs that he's going to confiscate all of it and wants Jeebs on the next transport off Earth or he will shoot him again. Kay and Edwards leave. Outside, two people on a tandem bicycle ride by, their clothing covered with lights. Kay tells Edwards that he can't help him get a handle on the moment, but says that the only comfort he can offer is his promise that tomorrow morning Edwards wont remember a thing. Edwards remarks that it's not exactly some stuff you just forget, then Kay zaps Edwards with the neuralizer.
Later, in a Chinese restaurant, Kay is telling Edwards some jokes. Kay looks at his watch then gets up to go. Edwards asks who he is, and Kay gives him his business card, to see him at 9:00. Kay leaves, and Edwards looks at the card, which shows "MiB" embossed on one side and "504 Battery Drive" printed on the other side.
A Zap-EM exterminator truck pulls up to a building. The exterminator opens the building door, and roaches scurry everywhere. He has a gas canister on his back with hoses attached and a gas mask pulled over his forehead. He tells Edgar that he has a pest problem. Edgar then refers to people as the infestation, "nothing but an undeveloped, unevolved, barely conscious pond scum, totally convinced of their own superiority as they scurry about their short pointless lives." Edgar then grabs the exterminator and kills him by forcing his gas pipe down his mouth. The man falls to the floor, dead, gas pouring out of his mouth. Edgar rolls the saucer into the back of the truck.
Edwards arrives at the MiB building and shows the card to the guard, who sends him to the elevator. Upstairs, Edwards doesn't notice that the elevator's back doors open until MiB chief agent Zed (Rip Torn) tells him that he's late. Five other men in military uniforms are already sitting there, and Edwards sits in the last chair. Zed tells them that they are there because they're the best of the best and MiB is looking for just one of them. Zed tells them he will give them some simple tests on motor skills, concentration, and stamina. Edwards raises his hand and asks why they're here, even though Zed already told them. 2nd Lt. Jake Jensen (Kent Faulcon) raises his hand and Zed motions to him to stand. Standing stiffly, he recites what Zed told them. Zed nods and he sits back down. Edwards chuckles then mocks Jensen and calls him "Captain America." Zed scowls at Edwards, and the others stare at him. Kay watches on the other side of a two-way mirror.
They start the written exam. In this one, Edwards breaks his pencil and tears the cover of his notebook as he tries to open it. All the men struggle to write in their awkward egg-shaped chairs, poking holes in the paper. Edwards puts down his notebook and pencil then drags the metal table from the center of the room to bring it next to his chair. The table makes a horrible scraping sound and the other men stop writing. Happy now, Edwards retrieves his notebook and pencil and asks the others if they want to use the table too.
The next test is a dark target range; a strobe light flashes, and cardboard alien figures move in front of the men. The other recruits shoot at every alien figure moving by, but Edwards waits, then fires a single shot. Zed stops the test and then with the remote brings the target forward that Edwards shot -- a little girl holding school books; he asks Edwards why he thought "little Tiffany deserved to die." Edwards tells Zed that she's the only one who seemed dangerous and explains his logic: target 1, which was hanging from a street light, was just working out; another one was snarling, but had a tissue in his hand -- he's sneezing not snarling; then he saw "little Tiffany -- 8-year-old white girl middle of the night in the ghetto among a bunch of monsters, reading quantum physics, and those books are way too advanced for her -- she's up to something." Zed just shakes his head and walks out. Edwards asks the others if it was a good shot. They shake their heads in disgust. Zed tells Kay that Edwards has a problem with authority; Kay replies that so does he (Kay), but Edwards ran down a cephalopoid on foot, which is tough. Zed hopes that Kay knows what he's doing.
Zed comes back into the room, and congratulates the men, telling then that they're everything MiB could expect from years of government training. He tells them to follow him for one more test -- an eye exam. They put down their pistols and follow him.
Edwards is the last one out. Kay stops him then hands him a folder and they walk down the hallway. Kay explains that in the 1950s the government established an agency to establish contact with races from other planets; they were surprised when aliens actually did contact them. Kay and Edwards pass a room, where Zed is administering the "eye exam" to the others with a neuralizer. The neuralizer flashes as Kay and Edwards continue down the hallway. Edwards opens the folder and sees a photo of an alien standing at the door of an alien spacecraft. Kay explains: in the mid-1950s, the government started an under funded agency to establish contact with races from other planets; aliens made contact on March 2, 1961. "There were nine of us the first night: seven agents, an astronomer, and one dumb kid who got lost on the wrong back road." One photo shows agents by an old pickup truck and its driver (who looks like Kay) standing by the front; the next one shows the pickup driver giving a tall alien some flowers as the agents look on. Edwards turns the page to the next photo, two disks atop towers. Edwards says, "Uh-huh, so, these were real flying saucers, and the World's Fair was just a cover-up?" Kay replies, "Why else would we hold it in Queens?" Edwards suggests that Kay get a CAT scan, then asks to be let out. Kay asks Edwards if he wants any coffee then opens the door to the break room, revealing four worm-like aliens with long legs drinking coffee. Edwards stares in shock as a worm pours coffee for Kay. Kay asks Edwards again if he wants coffee, but he just stutters, speechless.
Kay and Edwards sit on a bench by the waterfront. Kay tells Edwards that there are about 1500 aliens on the planet, and most of them are there in Manhattan. Most of them are decent enough, and are trying to make a living. Kay says that humans are for the most part clueless, and are happy not knowing about these things. Edwards asks why they keep it a secret, that people are smart and can handle it. Kay replies that a person is smart, but people are dumb, panicky, dangerous animals. He tells Edwards that 1500 years ago, everybody knew the Earth was the center of the universe; 500 years ago everybody knew the Earth was flat; and 15 minutes ago Edwards knew that people were alone on this planet. Kay sighs and says, "Imagine what you'll know...tomorrow." Edwards asks him what's the catch. Kay replies that the catch is he has to sever every human contact and no one will ever know he exists anywhere, ever. Edwards asks if it's worth it, and Kay says it is if he's strong enough. He gives Edwards until sunrise to think it over, and leaves. Edwards sits there until night.
At MiB headquarters, Edwards enters the elevator as Kay waits for him. Edwards says that he's in. He tells Kay that they chose him because they recognized his skills, and not to call him son or kid or sport. Kay replies that his skills now mean precisely nothing. The elevator's back doors open, revealing a large bay: Earth customs.
As Kay and Edwards walk, a customs agent asks a tall alien (Carel Struycken) if he has any fruits or vegetables, and he states that he's on a diplomatic mission. Edwards asks Kay what branch of the government they report to. Kay replies that there is none, because they ask too many questions. Edwards asks who pays for all of this. Kay tells him that they hold patents on some gadgets they confiscated from out-of-state visitors, such as Velcro, microwave oven, and liposuction. Kay and Edwards enter a room filled with alien technology. Kay shows him a small disk about 1-1/2 inches in diameter. Kay says that it will replace CDs soon, and he will have to buy the "White" album again. He then shows Edwards a universal translator. Edwards notices a sphere about the size of a golf ball floating in air a couple of inches above a metal stand. He reaches for it and knocks it away. The energetic sphere flies quickly out the door into the customs bay, hitting many things as it speeds away. People dodge as the sphere ricochets off walls, hits lamps and other things, then destroys a lab. Finally Kay catches it with a special mitt. As Kay puts the sphere back at its stand, he tells Edwards that it caused the 1977 New York City blackout (as a type of prank), then places the mitt next to the stand.
Kay tells Edwards that observation is the heart of their endeavor. He introduces Edwards to two multi-armed aliens: "the twins", "Blblup" and Bob. The twins sit at a control panel; the map shows the location of every registered alien on Earth; some of them are under constant surveillance. (Two of the aliens displayed are Steven Spielberg and Sylvester Stallone.) Edwards remarks that it makes sense, because when he was in third grade he knew his teacher had to be from Venus or someplace like that.
Zed interrupts them and tells Edwards to put "it" on: the last suit he will ever wear. Kay uses the computer to delete all of Edwards personal information, such as birth certificate, driver's license, etc. As Zed narrates, Edwards goes to his locker, labeled "J", and then gets dressed: "You will dress only in attire specially sanctioned by MiB special services. You'll conform to the identity we give you, eat where we tell you, live where we tell you." Edwards puts his hands on a metal sphere. The sphere scans his fingerprints and burns them off; he recoils in pain. Zed continues: "From now on, you'll have no identifying marks of any kind, you will not stand out in any way. Your entire image is crafted to leave no lasting memory with anybody you encounter. You are a rumor, recognizable only as déjà vu, and dismissed just as quickly. You don't exist. You were never even born. Anonymity is your name, silence your native tongue. You are no longer part of the system. You are above the system. Over it. Beyond it. We're 'Them'. We're 'They'. We are the Men in Black." Kay updates the database with Edwards' new name: J. As J, "Jay", puts on his sunglasses, he tells Kay that the difference between them is that "I make this look good."
G. Rosenberg (Mike Nussbaum) leaves his jewelry store, carrying his pet cat in a bag, and a small metal case. Edgar drives by the store and then adjusts his stiff joints as he observes Rosenberg. After Rosenberg locks the doors, Edgar drives away.
Zed briefs Kay and Jay on the status of some aliens as they watch a monitor. He tells them they had an unauthorized landing in upstate New York. Suddenly the alarm sounds below them: a boundary violation. Zed tells them that it's an alien named Redgick; he's not cleared to leave Manhattan, and is stuck in gridlock on the New Jersey turnpike. He tells Kay to take Jay with him so he can warm up on something. Jay mocks Zed as they walk to Kay's car. Jay complains that even though they have unlimited technology from the whole universe, they cruise around in a Ford P.O.S. They get in the car and Kay tells Jay to fasten his seat belt, but he doesn't. Jay tells Kay that he has to work on his people skills, that he would get a better reaction if he were a little more polite. Kay then asks him to please fasten his seat belt, and then drives away, the car racing like a dragster. Jay gets slammed around violently. Jay holds onto a lever protruding between the seats. Kay tells him to never press the red button on it, and Jay quickly lets go. They race down the road.
A taxi drops Rosenberg off at a restaurant. Edgar stops next to them, then drives away. Rosenberg enters the restaurant and sits with a tall humanoid alien, the one who Kay and Jay saw at Earth customs. Speaking in an alien language, Rosenberg tells the diplomat that he's late because of the cab driver. The diplomat calls Rosenberg "Your Majesty" and tells him that he's in grave danger. He says that a bug landed there and they have to get him off the planet. They both agree that the bug knows why Rosenberg is there. The diplomat thinks he recognizes the device (the metal case), but Rosenberg says that it's diamonds for the diplomat's children. The short-order cook says that their order is up, then wonders where Ivan is. Edgar says that he gave him a break. He takes the two plates to the table, passing Ivan, who is dead and stuffed between two shelves. The diplomat toasts to the continued reign of the Arquillian Empire. Rosenberg toasts to the safety of the galaxy. Edgar puts their plates down on the table, and then roaches come out of his sleeves onto the plates. Rosenberg looks up in fear, and then tells Edgar that he can kill them both but won't find the galaxy. The cat looks out of the bag. The word Orion is on its collar, and something hangs from it. Edgar tells Rosenberg that he's right about one thing. He kills the Arquillians, and then takes the case and rushes outside.
Kay stops a car, asking Reggie Redgick (Patrick Breen) for his license and registration as Jay looks on. Reggie shows Kay his driver's license and registration, then Kay asks for his other license and registration, which he then shows to Kay. Kay tells him that his resident alien card restricts him to the five boroughs. Kay asks Reggie where he's going, and then Kay and Jay see his wife in labor on the back seat. Kay takes Reggie back to the Ford, and tells Jay to handle the birth. Jay complains, but Kay tells him that it's easy and to just catch. Kay reassures Reggie that Jay does it all the time. Jay stands by the car and tries to coach the wife with her breathing. A tentacle comes out of the car and grabs Jay as Kay interrogates Reggie normally, completely oblivious to Jay's dilemna. Kay asks Reggie why he's heading out of town when Croagg the midwife is at 54th and Madison. Reggie tells Kay that they're meeting someone at a ship. Kay tells Reggie that he's not cleared for departure. Reggie replies that it's an emergency. As the tentacle waves Jay around high in the air, Kay reassures him that he's doing fine. The tentacle pulls Jay into the car then out on the opposite side. Kay asks Reggie why he's so eager to get off the planet, and he replies that they don't like the neighborhood because of some of the new arrivals. The tentacle slams Jay against the roof of the car, and then pulls him back in. Kay asks Reggie if it is related to the crasher from last night. Jay flies out of the car onto the grass, holding the tentacled alien baby. Kay congratulates Reggie on his... "squid", and gives him back his resident alien card. Jay says that the baby is cute, but it spits up on him while he speaks. Back in Kay's car, slime drips off Jay. Kay asks him if anything about that seemed unusual to him. Jay just turns and looks at him. Kay wonders what would scare Reggie enough that he would risk a warp drive with a newborn, and tells Edwards that he's going to check the "hot sheets."
Kay and Jay go to a newsstand, and Kay buys several tabloids. Jay can't believe this, but Kay calls them the best investigative reporting on the planet. He says that Jay could get lucky if he read The New York Times, then shows him the cover story of The World: "ALIEN STOLE MY HUSBAND'S SKIN!"
Kay and Jay drive to Beatrice's farm, posing as FBI agents who want to talk to her about her visitor. He assures her that they're not there to make fun of her, and she lets them in and gives them lemonade. She tells them that the chief of police made a full investigation and took a report, writing down everything she said; he didn't believe her, but instead made fun of her. She says that the chief asked how could Edgar walk back in the house if he was murdered, but she didn't know. She says that she knew it wasn't Edgar; it was like something was wearing Edgar, like a suit. Jay shows Kay a photo of Edgar, saying that he was that ugly before he was an alien. Beatrice says that when she woke up, he was gone. Kay asks her if he said anything, and she replies that he asked for sugar water. Kay signals for Jay to put on his sunglasses and then Kay zaps her with the neuralizer. He tells her that there was no alien; the flash of light she saw in the sky was not a UFO; swamp gas from a weather balloon was trapped in a thermal pocket and it refracted the light from Venus. Jay can't believe that Kay could do that and give her another memory, and that's the best he could come up with. Kay continues adding to her fake memory, saying that Edgar ran off with an old girlfriend, and that Beatrice should go to her mother's for a couple of nights. Jay adds that he never appreciated her anyway; that she kicked him out; and that she should go to Bloomingdale's. He finishes with telling her to hire a decorator. Outside, Kay scoops up some dirt from the crater into a pocket analyzer. Jay asks Kay when he's getting his own "flashy little memory messer-upper thingy" (neuralizer); Kay replies that he will when he grows up. The analyzer's green light comes on, and Kay asks Jay if he knows what kind of alien life leaves a green spectral trail and craves sugar water. Jay jokes that it was on "Final Jeopardy" last night. Kay calls Zed and informs him that they have a bug. Jay wonders how that's bad. Kay explains that bugs thrive on carnage -- they consume, infest, destroy, and live off the death and destruction of other species. Kay tells him to imagine "a giant cockroach with unlimited strength, a massive inferiority complex, and a real short temper... is terror-assing around Manhattan in a brand new Edgar suit." Kay tells Jay that they have to watch the morgues.
A cop wheels Rosenberg's corpse into the morgue; Rosenberg's cat sits on top. The medical examiner, Laurel Weaver, takes the corpse to the back and performs an autopsy on it. The other dead Arquillian is at the freezers. She looks in disbelief at his insides, and asks him what he is. Kay and Jay enter the morgue building. Weaver dictates her findings into a recorder (paraphrased): "The subject's temperature rose up to 112° at the time of autopsy; when I tried to verify this rectally, I found that he didn't have a rectum, which is..." Kay finishes for her with, "Weird." He introduces himself as Dr. Leo Manville, Department of Public Health, and Jay as Dr. White. Kay asks her if she has anything unusual there. She replies that it's a triple homicide; the first body she opened was normal, except that it was broken in half. She shows them the tall Arquillian. She says that he has a skeletal structure unlike anything she saw before. Kay says that he'll look at it, and then Weaver takes Jay to look at the other one (Rosenberg), which she says is even stranger. With gloves on, Weaver and Jay explore his insides. She asks him if he notices anything strange -- stomach, liver, and lungs. He says that they're all fine, but she tells him they are all missing. He makes up a lame explanation for his examination. She asks if they met before, and says she has a strange feeling of déjà vu; Jay says that he does too. She tells Jay not to tell "the other guy" (Kay) that she thinks the body is not really a body but is a transport unit for something else. She starts to tell him what she likes to do sometimes "when it's really late", but Kay calls him over. Looking at the dead tall alien, Kay asks Jay what he thinks, but Jay mistakenly talks about Weaver and her body. Kay tells him," the dead body," and Jay says that Kay should look at the other one. Jay recognizes the tall alien from headquarters. Kay asks him what killed the alien; Jay correctly answers that a bug did. Weaver calls Jay back. She shows him wires protruding from one of Rosenberg's ears. Jay pulls on the ear lobe; the ears eject, and high-pressure air vents from them. The face swings open to reveal a tiny alien inside the skull, seated at a control console surrounded by lights. The tiny alien draws in labored breaths and says, "Must...to prevent...contest." Jay and Weaver coach the alien into saying the right words: "To prevent war." They help the alien finish his sentence: "The galaxy is on Orion's belt." The alien dies and then the lights inside the skull turn off. Jay wonders what it means and calls Kay, "Doctor whatever" over. Weaver realizes that they aren't from the Department of Health. Kay says, "Rosenberg." He sees the open skull and says that the Arquillians won't like it because he was from the royal family. Weaver declares that it's an alien, and Kay and Jay are government agents hiding the facts. Jay tells Kay what the alien said: "To prevent war, the galaxy is on Orion's belt." Kay puts on his sunglasses, prompting Jay to puts his on too. Kay zaps Weaver with the neuralizer. Kay says that it doesn't make sense. Weaver recovers and asks for their ID, and Kay zaps her with the neuralizer again. Jay thinks it will give her brain cancer. Kay tells Jay that they have to leave and close all the doors because Special Services will be there soon. As they leave, Jay asks Kay if he zapped him with it, and Kay tells him no. Jay asks to be in charge of the neuralizer, but Kay says no. They pass two MiB Special Services men outside, and Kay briefs them on the situation. After Jay complains, Kay tells them to give Weaver a happy memory.
In a back alley somewhere, Edgar struggles violently in the Zap-Em truck to open the Arquillian's case. He finally breaks it open, spilling diamonds on the floor. He growls in frustration, "Where is it?"
Kay and Jay return to MiB headquarters. Kay uses the satellite to locate and zoom in on his wife he had before he joined MiB. Meanwhile, Jay asks Zed if anyone there ever gets any sleep. Zed replies that "the twins" keep them on Centaurian time, a 37-hour day. Zed tells Jay that he will get used to it in a few months, or have a psychotic episode. Pointing to a large display, Zed shows Jay where Orion is. He explains that Orion's belt is only 3 stars, not a galaxy, and that there are no galaxies on Orion's belt. Zed tells Jay that he heard wrong, but Jay insists that he heard it correctly and leaves. As Kay freezes the image of his wife on the monitor, Jay calls her pretty, and Kay clears the screen. Jay correctly concludes that Kay was the person giving flowers to the tall alien in the photograph; his wife never got them and she never remarried. Zed calls Kay over to look at the twins' display: all the aliens are leaving the United States. Jay wonders why, and Kay compares it to rats deserting a ship. Kay uses a satellite to locate an Arquillian battle cruiser in space. Zed says they (MiB) have a dead Arquillian prince. The Arquillian ship sends a message, and Zed tells the twins to translate it. He then sends Kay and Jay to Rosenberg's jewelry store to try to find information. As they leave, Zed tells Kay to give Jay a weapon.
At the armory, Kay takes a "Series 4 De-atomizer". Jay thinks it's for him, but Kay gives him a very small pistol -- a "Noisy Cricket". Jay complains, calling it a midget cricket and waves it around, but Kay grabs his arm and stops him. As they leave, Jay tells Kay that he might break it.
Edgar parks across the street from Rosenberg's jewelry store and breaks in. He smashes all the jewelry cases, looking for the missing galaxy. Outside, a tow truck driver hooks up the Zap-Em truck. Edgar sees a photo of Rosenberg holding his cat. He also sees another photo of the cat, and focuses on the spherical object hanging from its collar. Edgar goes outside and tries to stop the driver from towing the truck. Kay and Jay arrive at the store and see the mess. Jay wonders who would do that but not take the jewelry; Kay tells him that it's someone who wasn't looking for jewelry. Jay sees the photos and remarks that Rosenberg "had a serious crush on his cat." Edgar shoots the tow truck driver. Jay shoots at Edgar. The blast throws Jay against a wall and destroys the storefront. Jay runs outside and shoots at Edgar again as he drives away in the tow truck. The blast disconnects the Zap-Em truck and throws Jay into some trash bags and cans. Jay stands on a car and shoots again at the tow truck as it turns the corner. He misses, blowing a giant hole in a tractor-trailer. The recoil throws Jay onto a car's windshield. Kay pulls him off and tells him that they don't discharge their weapons in view of the public. Jay reminds Kay that the alien ship is about to... Kay interrupts him, saying that there's always an alien emergency on Earth; the only way people remain happy is because they don't know about it. Kay tells Jay that the bug isn't leaving because they have his ship. Jay goes to the Zap-Em truck and pulls people out of it. Kay calls Zed for a containment crew, but Zed replies that it's a moot point because the exodus continues. The monitor at MiB shows the translation of the Arquillian message: "MIB DELIVER THE GALAXY". Zed sees the worm aliens leaving and shouts at them, calling them sorry little ingrates. They are leaving with their luggage and 5 cases of Marlboro cigarettes. They tell him off in their language and laugh. Zed tells Kay that they've only translated part of the message, but the Arquillians hold MiB responsible.
Edgar gets out of the truck. A street vendor sits next to his wares: various bug-killing devices such as fly swatters, Combat, and Raid bug spray. Edgar asks the man where he keeps his dead, who says that he doesn't have any dead. Edgar chokes him, so the man says that they're at the city morgue. Edgar knocks over one of his stands and takes some postcards, and then he leaves.
Jay is trying to give a normal explanation to the crowd for what just happened, but Kay calls him over. Kay tells Jay that the Arquillians want the galaxy, whatever that means. He says that they need some help from a professional, someone who has years of experience in intergalactic politics. Kay hopes that "the little twerp hasn't skipped town." A man from MiB Special Services announces on a loud speaker for the crowd to gather around and look at his neuralizer.
Kay and Jay stop at a locksmith's shop. Jay thinks that the creepy-looking owner is an alien in disguise, but his pet pug speaks, telling Jay, "If you don't like it, you can kiss my furry little butt." Kay talks to the dog, Frank (voiced by Tim Blaney), who says that he's busy. Kay grabs Frank, and threatens to call the pound. Jay tells a passing man that the dog owes his friend some money. Kay asks Frank what he knows about Arquillians and bugs, but he pretends he doesn't know. Kay shakes him, then Frank says that Rosenberg wasn't an ordinary Arquillian; he was the guardian of a whole galaxy; they thought he would be safe on Earth. Frank says that the galaxy is the best source for subatomic energy in the universe; if the bugs get it, the Arquillians are doomed. Kay asks Frank about a galaxy on Orion's belt. Frank pretends he doesn't know, until Kay shakes him again. Some people have gathered across the street. Jay tells them that they're rehearsing for a ventriloquist act. Frank finally says that the galaxy is here. Jay replies that a galaxy is hundreds of millions of stars and planets; how could it be here? Frank tells them that size doesn't matter; just because something is important doesn't mean that it's not very small. Kay shakes him and asks him how small. Frank replies that it's tiny, like the size of a marble or jewel. Frank says that he has to be walked before his flight, so Kay lets him down and he runs away. Kay tells Jay that if the galaxy's there, it's not on Orion's belt. Frank stops to bark at a cat up on a ledge with a bell on its collar. Jay sees the cat and realizes what Orion is; he calls Kay.
At the morgue, the cat runs across the floor then jumps onto Laurel Weaver's desk, startling her. She reads the collar and says that Orion is a pretty name, and then grabs the small spherical object hanging from the cat's collar. She says, "Wow" when she notices the galaxy rotating in the sphere, then stares at it, mesmerized at the galaxy as it reflects brightly in her eyes.
Edgar goes to the morgue and sets his rifle down. He rings the bell several times, and then Orion hisses and runs away. The morgue attendant (David Cross) comes to the desk and berates him for ringing the bell too much. Edgar asks to see his dead friend and the cat he gave him; he wants the cat back. The attendant asks for proof of ownership, relationship to the deceased, etc. Edgar gets upset when the man swats some flies. Several roaches crawl out of Edgar's sleeve, so the man gets some bug spray. Edgar stares angrily and growls at the man, and he trembles in fear.
Kay and Jay arrive at the morgue. Jay says that he wants to handle it, because he doesn't want Kay to zap Laurel with the neuralizer again and give her brain damage. Kay gives him two minutes. Inside, Edgar throws Laurel against the freezers and Orion hides. Edgar asks her where the cat is, but she doesn't know. He drags her across the floor, looking for the cat, but stops when Jay rings the bell and calls out. Jay gives up when no one comes over, so he goes inside. He finds Laurel behind a cart and tells her that he's Sergeant Friday from the 26th precinct. He asks her if she saw a cat that came in with a corpse; the cat's nametag said Orion. She replies that she did. Jay tells her that he needs to take the cat because it's a witness in a murder case and he'll ask it some questions. She says that she doesn't know where it is right now. He's surprised, but she coyly asks him to take her instead. Jay flirts with her, unaware that Edgar is hiding under the cart. Kay enters the morgue building, looks around, and then looks at his watch. Laurel points down, saying that she needs to show him something. Jay misunderstands her double entendre, saying that she's going too fast. He flirts with her some more. Kay lights a match to smoke a cigarette, but ooze drips from the ceiling and puts it out. He looks up and sees the attendant stuck to the ceiling, along with the bug spray and some papers. Laurel repeats her request, backing up and pointing, and Jay finally understands and draws his weapon. Orion jumps onto the cart, and Edgar grabs the cat and hides behind Laurel. Kay bursts in and joins Jay, pointing his weapon at Edgar. Laurel calls Jay thick, and they argue. Edgar tells her to shut up. He tells them that compared to them, he's on the top rung of the evolutionary ladder. Kay and Jay back him up towards a wall. Kay asks him how far he'll get without his ship. Edgar jumps with Laurel through a window up to street level. Kay and Jay run to catch up with them. Edgar hijacks a taxi, kicking the driver out with his prayer rug. He tells Laurel to take him to the place on a postcard he holds up (the World's Fair), but she refuses. She floors it when bugs climb out of his mouth. Edgar swallows the galaxy. When Kay and Jay get outside, Jay sees the prayer rug and tells Kay that Edgar is in a cab then runs after them. Jay comes around the corner and sees many taxi cabs stopped at a signal. He points his weapon at the people in one, but it's not the right taxi, so he walks away in frustration. Kay drives up and picks up Jay and then they drive away.
At MiB headquarters, Kay tells a man to put up a bio-net around Manhattan. The Arquillians fire a warning shot at the North Pole. Kay tells Jay that it's Arquillian battle rules: after the ultimatum they fire a warning shot and give Earth a galactic standard week to respond -- one hour. The screen shows the fully translated message: "MIB: DELIVER THE GALAXY OR EARTH WILL BE DESTROYED. SORRY". Kay tells Jay that to keep the bugs from getting it, the Arquillians will destroy that galaxy. Zed adds, "and whatever planet it's on." As Kay and Zed speculate on the ships that Edgar would try to take, Jay shouts to the "old guys" and calls their attention. Everyone stops and turns as Jay asks them if "those" still work, referring to the towers at the World's Fair.
Laurel and Edgar arrive at the World's Fair. He tells her that he took her with him because he needs "a snack" for the long trip. Kay and Jay drive to Queens, but Jay says that the tunnel will be packed. They enter the tunnel and Kay tells him to press the red button. The car transforms into a jet car and Kay tells Jay to put on his seat belt, but he doesn't (again). Jay screams as the car speeds towards traffic, then climbs a wall and flies upside down. Jay gets slammed against the roof of the car. Kay puts an 8-track tape in the player for music to help Jay relax: Elvis Presley singing "Promised Land". As Jay struggles to find a more comfortable position, Kay sings along with Elvis. They dodge a sign on a truck then climb down the wall, landing on the road outside the other end of the tunnel.
Edgar climbs a ladder on one of the towers, holding Laurel. She tells him that he wouldn't want to eat her because she's a very important person, like a queen or a goddess, and it could start a war. He replies that it's good, and will mean more food for his family -- all 78 million of them. Laurel jumps into a tree so he lets her go. When he reaches the top, he opens a panel in the saucer and enters it. Kay and Jay pull up. Kay takes two large weapons from the trunk and gives one to Jay. Kay says, "Roaches check in," and Jay finishes, "but they don't check out." They walk to the tower.
The saucer halves close and it lifts off the tower. It flies over Shea Stadium, where the Mets are playing. An outfielder becomes mesmerized by the saucer, and a fly ball beans him. Kay and Jay shoot the saucer with their pulse rifles and it explodes into flames. It flies out of control and crashes through the Unisphere, stopping a few feet in front of them. The door opens and Edgar staggers towards them, barely recognizable. Kay tells Edgar that he's under arrest for violating the Tycho treaty. Jay orders him to turn over the galaxy, step away from the vehicle, and put his hands on his head. Edgar puts his hands on his head, but then rips off his skin and head, revealing his true form: a giant monstrous cockroach. The bug snarls and eats their weapons then knocks them to the ground, roaring. Kay gets back up, telling Jay to keep the bug from getting on the second ship and to keep him on Earth. Kay tells Jay that he's going to get his gun back, and Jay gets up. Kay confronts the bug, calling him a slimy, gut-sucking intestinal parasite. He shouts at the bug to eat him, and it does, roaring and swallowing him whole. It roars again and walks to the second tower. Telling the bug that it forgot dessert, Jay throws a large rock at its head. He tries repeatedly to stop it, but it keeps knocking him down. The bug starts climbing the tower, but Jay grabs its hind end. It shakes him loose, throwing him against a dumpster. Laurel falls to the ground and hides. Jay gets up and tries to goad the bug into fighting some more, but he notices cockroaches on his sleeve. He kicks open the rusty dumpster and many more roaches spill out. He purposely steps on a cockroach and the giant bug stops. Jay taunts the bug, calling some roaches his aunt and uncle. He steps on another one and the giant bug jumps back down off the ladder. Jay continues to step on roaches as the bug walks towards him. Jay tells the bug to ease off of his face before something bad happens to him. Kay's weapon whines and the bug looks at its gut before Kay blasts it in two. Kay lands next to Jay; both of them are covered in slime. Jay picks up the galaxy off the ground, and Kay calls Zed and tells him to inform the Arquillians. They don't notice movement behind them. Jay tells Kay that while he was in there playing around, he was doing all the work. Jay tells Kay what he did and gives the galaxy to Kay. Kay tells him that he should have been there for the 1968 Zeronian migration, but then realizes that Jay wasn't even alive then. The giant bug isn't dead yet, and rises up to eat Jay, but someone blasts it with a pulse rifle, killing it. They turn around and see Laurel holding the rifle.
Kay and Jay have cleaned up and returned to MiB headquarters, standing outside. Laurel waits by the car. Kay takes out his neuralizer, but Jay complains that she helped them. Kay says it's not for her; it's for himself. Kay looks up at the stars and tells Jay that he never looks at them anymore and that they're beautiful. He tells Jay that he hasn't been training a partner; he's been training a replacement. Jay complains that he can't do this job alone. Laurel interrupts, saying that her apartment isn't near there, and not even on the same island. Kay adjusts the dials on the neuralizer, then shows Jay the days, months, and years dials on it, and tells him to always face it forward. He hands it to Jay. Jay tries to object, but Kay says that being down the gullet of an interstellar cockroach is one of a hundred memories that he wants to forget. Jay puts on his sunglasses. Kay tells Jay that he'll see him around, but Jay replies that he won't and zaps him with the neuralizer.
The New York Post reports that Detroit has a car that defies gravity. The Weekly World News reports: "N.Y. Mets centerfielder says 'UFO MADE ME MISS HOME RUN!'" The Enquirer reports that a man awakens from a 35-year coma; it has a photo of Kay standing with his wife while giving her flowers. Jay chuckles as he takes all three newspapers. He puts his dark sunglasses on then turns around when Laurel calls him. He walks back to the car from the hot dog stand carrying two hot dogs. She's dressed in a black suit and is now one of the MiB, and tells him that Zed called: the high consulate from Solaxiant Nine wants floor seats for the Knicks-Bulls game. Jay tells her that they'll call Dennis Rodman because he's from that planet, and gives her the hot dogs. She remarks that it's not much of a disguise. They drive away.
The view zooms out from Manhattan, Earth and the Moon, then the solar system and the entire Milky Way Galaxy -- revealing the galaxy to be inside a sphere like a marble. An alien hand picks up the "marble" and throws it against another "marble" (galaxy) as if it's playing a game of marbles, then picks them both up and puts them in a cloth sack containing several other "marbles" (galaxies).
Will Smith sings "Men in Black" during the end credits.