The story opens with a man sleeping in a remote cabin in the American Old West. The door to the cabin bursts open and a gunman enters, shooting at the sleeping man, who quickly grabs his pistol and shoots back, killing his would-be killer. The man continues to aim at the sides of the cabin and shoots another man walking outside. Repeated shotgun blasts blow through the roof of the cabin but the man is out of shots for his revolver. He tosses the revolver at the wood burning stove in the cabin and distracts the roof shooter long enough to grab his Winchester rifle. He shoots upward and hits the roof shooter, who falls into the cabin. The man with the rifle, Emmett (Scott Glenn), walks outside and looks over the failed assassins. He also looks at the horses, seeing a familiar brand emblem. Emmett leaves the cabin and continues his journey, taking the branded horse with him.
Far out in the desert, he comes across another man, lying on the ground in his long underwear. He gives the man some water and takes him along. Later, as they camp for the night, the man in the underwear tells Emmett that his name is Paden (Kevin Kline) and that he'd been riding with a group of men who looted him and stole his horse. The two stop at an Army outpost where Emmett gives Paden some money to buy proper clothing. Paden suddenly spots his horse and the man who stole it. He ducks into the nearby general store where he has an argument with the shopkeep: lacking enough money to buy a pistol Paden wants to borrow one but the clerk won't let him. Paden asks the man for a gun worth the money Emmett gave him and is given a rusty old pistol that the cylinder falls out of. Paden rushes out to the square and loads the gun; he is spotted almost immediately by the horse thief, who rides toward him, shooting. Paden takes quick but very careful aim and shoots the man off the horse. A few minutes later, while he kisses his horse, Paden is grilled by a US Army sergeant about the shooting. Paden tells the lieutenant to look at the underside of his saddle, where his name is etched. When the lieutenant asks Paden his name, another man in the crowd, Cobb (Brian Dennehy), speaks up and tells the lieutenant how to spell it. The lieutenant checks the bottom of the saddle, confirming Paden's claim and tells the crowd to disperse. He also tells Paden to get some clothes.
Cobb loans Paden money to buy clothes and a hat (that has a humorously bent brim). Paden promises to pay Cobb back ("I'm good for it."). Cobb asks Paden to join him in a new business venture further out west. Paden refuses to join Cobb but watches as Cobb meets a scruffy, shady-looking man, Tyree, who's shackles are being removed while he's freed from custody. While Cobb and Tyree ride off, Tyree, in a sinister tone, asks Paden about a dog.
Emmett plans to ride to another remote town called Turley, where he'll pick up his brother, Jake (Kevin Costner), and continue to Silverado to meet their sister and her family. After they visit for a while, Jake and Emmett plan to move on to California. Paden agrees to go, especially after Emmett mentions that there's a saloon there, his favorite place. The two arrive and are immediately scolded by a grizzly man, Hobart, who mistakenly calls them Baxter and Holly. Hobart is leading a group of farmers who are heading to Silverado to settle. When the real Baxter and Holly arrive, Paden and Emmett are suspicious of the deal they strike with Hobart.
Paden and Emmett sit down to eat in a hotel restaurant. While they eat, a large black man, Malcolm "Mal" Johnson (Danny Glover) walks in and asks for a room for the night and a bottle of whiskey. The woman behind the counter apprehensively gives Mal the whiskey, however the hotel manager tells Mal to leave, saying he doesn't serve Mal's "kind" there. Three other man, eating at another table, suddenly stand up and approach Mal to throw him out. However, Mal is much tougher and smarter and quickly beats all three in a brief fight, causing a fair amount of damage to the restaurant. Just then the town's sheriff, John Langston (John Cleese), walks in and stops the brawl. Though Emmett and Paden offer testimony that Mal didn't start the fight, Langston still orders him to leave town without paying for the damage to the bar, knowing the manager's reputation for bigotry. Mal gathers his things and leaves, taking the only shot of whiskey that wasn't broken in the brawl. Langston sits down with Emmett and Paden, explaining despite his British ancestry, the people of Turley accepted him for maintaining the peace. To that end, he asks them why they're in town. Emmett tells him that he's meeting his brother, Jake, and when he describes him, Langston immediately knows where he is; Jake has been jailed for shooting a man. Jake tells Emmett that it was self-defense (for kissing the wrong woman), however, Langston seems driven by Old West justice and Jake is to be hanged the next morning at 10 am. Though Emmett tells Jake that he can't help him, after he leaves the sheriff's office, Emmett tells Paden he plans to bust Jake out. Paden, however, refuses to get involved and he and Emmett go to the saloon for a drink. In the saloon, Paden spots the man who stole his hat. He also surmises that the man is carrying his Colt revolver. The man stands up slowly and tries to draw but Paden is faster, and he kills him. Langston has Paden thrown in jail with Jake immediately.
The next morning, a young boy calls the sheriff out of his office. Langston leaves his deputy behind and follows the boy out; the sheriff's gallows where he'd planned to hang Jake, are engulfed in flames. Back in jail, Jake picks the cell's lock with his belt buckle. When the deputy cautiously enters the cell to investigate he sees only Paden standing there. He's just finished locking Paden's wrists to the cell bars when a boot drops into sight, behind Paden. Paden suddenly punches the deputy, knocking him cold. (Jake had been hiding piggyback on Paden.) The two find their gear and wait outside the sheriff's office for Emmett. They get into a brief gunfight with a few of the town's residents and Langston, who had returned from the burning gallows. Emmett arrives with a couple of horses and the three race out of town, with the sheriff and his posse close behind. When they reach the town's outskirts, Jake, Emmett and Paden are aided by Mal Johnson, hiding in a rock outcropping and shooting with a Henry rifle - Mal is an accomplished sniper and prevents Langston's deputy from shooting Jake and shoots Langston's hat off his head. Knowing that any further pursuit would be dangerous, Langston calls off the manhunt. Mal joins the three and they continue to Silverado.
Some time later the team finds Hobart's party, stranded in the scrubland. Baxter and Holly have betrayed them and stolen the strongbox with all their money. The team leaves Jake behind to get the wagon train moving again. Paden, Mal and Emmett ride north, finding a canyon where Baxter and Holly have joined up with their own gang. Emmett rides into the canyon, towing Paden's horse with Paden slung over it, playing dead. Emmett tells the gang's leader, Dawson (James Gammon), that he needs a place to hide out from a posse after robbing a bank in Turley. Dawson is furious that Emmett led a posse to his best hideout and plans to shoot Emmett on the spot when shots are heard from above. Mal and one of the settlers are shooting from the top of the canyon. Emmett frees all of Dawson's stolen horses, causing a ruckus, while Paden ties a rope to the strongbox and rides out, towing it behind him. Emmett follows with Mal and the settler covering the escape. While the three laugh over how well Mal's plan worked, the settler believes they'll betray him and his friends as well, and orders them to hand over the box. He's suddenly shot dead by one of Dawson's men who'd been hiding in the rocks above them; the three return fire and kill him. They ride back and help Jake guide the wagon train to Silverado. That night, Mal, Jake and Emmett share a campfire and Paden hints that he's interested in a woman named Hannah (Rosanna Arquette), the wife of the man who was killed at Dawson's hideout. Mal talks about the horrible work he endured in the slaughterhouses in Chicago and how he's going to Silverado to reunite with his father and his sister on the farm his father has set up.
The team guides the settlers to their territory and ride the rest of the way to Silverado. They go their separate ways. Paden goes to the local saloon and is awed when he meets the woman who manages it, Stella (Linda Hunt), who is a former legendary dancer from Virginia, the Midnight Star. She and Paden bond immediately, becoming instant friends. They're both met by Cobb, who reveals that he's sheriff of Silverado, calling the place "heaven." Mal goes to his father's farm, finding it overrun with cattle. He finds his father, Ezra, hiding out in a nearby cave; Ezra had been run off his land by by the men of a powerful cattle driver named McKendrick (Ray Baker). Ezra also tells Mal that his mother had died of fever the previous summer and that Mal's sister, Rae, is now a prostitute in town. Mal vows to set things right. At Jake and Emmett's sister's house, they reunite with their family. Their brother-in-law, the town's land claims agent, tells them that the town has become corrupted by Cobb's influence. Jake and Emmett are still determined to continue on to California.
At night, Mal's father goes out to a nearby stream for water. He's met there by two of McKendrick's men who steal his Henry rifle and kill him. Mal, asleep in the cave where his father had been hiding, hears the gunshots and races down to the stream to find his father dead and his Henry rifle stolen.
In town, Cobb meets Paden at the saloon and fires Stella's partner, Kelly, giving his job, security chief for Stella, to Paden. Cobb accuses Kelly of skimming profits and throws him out of the saloon. Paden accepts the job just as Kelly tries to shoot Cobb; Cobb is quicker on the draw and kills Kelly. Paden is unsure of having Cobb as a boss. While a crowd stares at Kelly's body, a professional gambler, Slick (Jeff Goldblum), arrives and inquires about a honest game. Cobb tells him to talk to Paden.
Mal goes into town to tell his sister, Rae (Lynn Whitfield), that their father is dead. Rae is mostly unconcerned and isn't happy to see her brother. Mal tries to convince Rae to give up prostitution but she refuses.
The settlers that were guided to Silverado hold a large picnic, inviting their rescuers, Jake and Emmett. During the festivities, McKendrick's men attack them, shooting their dogs and livestock and setting fire to their houses. Several people are shot. Jake and Emmett shoot several of the thugs; Emmett recovers a Henry rifle from one of them.
Back at the saloon, Stella and Paden discuss the liquor she sells, which she shamelessly dilutes, claiming the undiluted spirit is too dangerous. She shows Paden the bottle of the "good stuff" she keeps for special occasions. A disturbance in the bar gets their attention and Paden finds Jake and Cobb's man, Tyree, facing off against each other. Jake had kissed Tyree's woman, Phoebe, angering Tyree. Paden disarms the situation quickly, seizing Tyree's pistol and telling Jake to leave, reminding him about his arrest in Turley. He gives Tyree his gun back, Tyree immediately shoves it underneath Paden's chin, threatening to kill him. Stella talks him down and Tyree leaves.
Emmett and Jake's nephew, Augie, rides around town on a horse and is stopped by McKendrick and some of his men. Emmett happens by and returns the horse to McKendrick when he sees the cattle rancher's brand on it, proving the men who attacked Emmett while he was sleeping worked for him. McKendrick was looking for revenge, given Emmett shot his father to prevent him from shooting Jake in the back. The two exchange wary looks and McKendrick rides off.
At the saloon, Cobb tells Stella about his history riding with Paden: the two, along with a large group of thieves, had pulled off many robberies together with a small group of friends, including Tyree. A stray dog had joined the group, becoming their mascot. Following a robbery, the dog tripped up Tyree's horse, throwing him off. Tyree had shot the dog and Paden, who never cared for much more than himself, was overcome and stopped to take care of the dog. He was left behind by Cobb and the others, got arrested by the posse & served jail time. Following his telling of the story, Cobb gives Paden his first earnings in the saloon. Cobb suggests that Paden could run the saloon without Stella, however, Paden refuses, saying he'd quit before taking Stella's dream away from her. Cobb tells Paden that Emmett, Jake and Mal are causing trouble in his town. He asks Paden not to interfere with his handling of the situation and Paden agrees.
Outside town, Emmett is practicing his shooting, using Mal's father's rifle and his own pistol. When he's out of shots, several of McKendrick's men appear, including Tyree, throwing lariats around him, holding him down while Tyree runs him down with his horse. Just as they're about to shoot him dead, Mal appears on a nearby bluff and shoots one of Tyree's men in the hand, and kills another. They're sent back to town on foot. Mal talks to Emmett, telling him that he was looking for him and his father's rifle. Emmett is horribly injured but still needs to find his brother, who will be McKendrick's next target. Mal tells him to stay and rest and that he'll find Jake. Emmett tells him he's in just as much danger for killing the McKendrick's men.
Mal talks to his sister, telling her that the men who killed their father are after Jake. Rae has Slick meet Mal, with the time and place to find Jake. When Mal arrives there, Cobb is waiting and has Mal beaten and arrested. While incarcerated, Paden visits Mal, who is distrustful of his friend since Paden works for Cobb.
At Jake and Emmett's sister's house, McKendrick has captured them and waits for Jake. Jake returns home and is immediately captured. After he's brought outside, the house is set on fire to burn the land registries. His brother-in-law tries to stop McKendrick's men and is shot. His wife is knocked unconscious as well and Augie is kidnapped, having seen who caused the fire. News of the fire soon reaches the saloon. Paden and Stella rush to the fire; Stella directs her men to help with a bucket brigade headed by Paden, however, the fire has burned beyond control. Cobb appears and says how he hates to see such destruction in his town. He again warns Paden that any interference could be dangerous for Stella.
While Stella grills Paden on why he was just sitting around with everything going on, Rae gets word of her brother's capture and steals Slick's dagger, which he conceals in his boot. The deputy Mal shot in the hand brings her to him and tries to "search" her. She stabs the man in the back with Slick's dagger but is shot. Mal grabs the man and forces the dagger deeper into his chest, killing him. As he struggles for the keys to his cell, another of Cobb's deputies enters the room. Mal, virtually unable to see the man at an angle, throws the dagger into his chest, killing him. Meanwhile, Stella figures out why Paden wouldn't act: Cobb was using her as leverage. She said there are always people in the world who think they can push others around. Paden admires her spirit but is still afraid of Cobb hurting her. (STELLA: He can't hurt me...if he's dead.) Phoebe then arrives to show them that Mal freed himself and left his unconscious sister in the storage room.
Mal goes back to the cave where he'd left Emmett and tells him the evening's events, particularly about Augie being kidnapped. Overcoming his injuries, Emmett rises to his feet and gears up. Mal does as well, taking both his and his father's rifles. The pair ride out and are joined by Paden. They ride out to McKendrick's house on his cattle ranch. Causing a massive cattle stampede, they take out most of McKendrick's men. Mal takes up a position on the roof of the rancher's house, providing sniper cover fire. Emmett rides to the house and finds his nephew, killing several men. Augie tells Emmett that Jake was killed on the way to the house when he fell off his horse and into a deep ravine. Emmett smiles, knowing that Jake, an acrobat of some talent, would never have such an accident and likely faked his own death. Paden battles several more men in the horse barn and is nearly shot when one thug sneaks up on him with Jake's pistols. As he moves in, Jake swings down on a rope, knocking the man out cold. The two take out the rest of the men in the barn and retreat, Jake finding both Augie and Emmett at the house. Mal is nearly killed himself on the roof, however, he is able to take out his killer after a warning from Paden. The team leaves the ranch and rides for Silverado.
At the outskirts of town, the team gears up and leaves Augie at the town cemetery. All four settle their personal scores with Cobb's men: Jake rushes into the saloon, drawing the attention of Tyree and another deputy. The two search the saloon but can't find Jake, who'd been hiding under the platform that Stella has behind the bar. Jake, having removed his boots, sneaks out to find that Tyree and his partner have walked down opposite sides from the front door. Jake calls out to them and shoots them both simultaneously.
Mal goes to the store room where Rae lies injured. Slick is there, having traced Rae. Slick, telling Mal that Rae needs a doctor, tries to kill Mal with a hidden Derringer, however, Mal is too fast. Slick reaches for his dagger, but Mal buries it in his stomach.
Emmett rides through town looking for McKendrick and the two begin a furious horseback gunfight. Emmett is able to take out McKendrick's sniper, but loses his rifle when McKendrick lands a lucky shot, jamming it. Emmett is also shot in the leg by his enemy, dropping his pistol. Emmett lures McKendrick to the other side of town; riding his horse up a loading ramp, he makes his horse jump from a platform, it's hooves hitting McKendrick in the head, unseating & killing him.
Paden and Cobb face off in a traditional Old West duel, with Stella looking on. The two say goodbye to each other. Cobb draws first, but is too slow and Paden kills him. Paden slowly re-holsters his pistol.
Paden and Stella meet back in the saloon and finally share a drink of the "good stuff." Emmett and Jake say their goodbyes as well and head out for California, like they planned, their brother-in-law and sister and Augie are safe. Mal and Rae head back to their father's farm. As they all leave, Paden now wears the Silverado sheriff's badge and seems likely to marry Hannah, the settler.