In the opening scene, there is a bus just crossing over the Iranian border. A woman, Scarlet Marlowe (Perdita Weeks) is speaking into her camera, saying she has come to Iran to search for a piece of history about to be lost in a hidden catacomb that is about to be demolished by the government. She tells the camera that she understands that she is putting herself in great danger and potential execution by the Iranian authorities by trespassing where she doesn't belong but slyly notes "They'll have to catch me first."
Scarlet goes to the home of Reza (Hamid Djavadan) a man who is willing to help her. His home actually has access to the catacomb Scarlet wants to enter. Reza tells her they have to be quick as the government cannot see them and the demolition is going to happen very soon.
Scarlet and Reza go down but notice soldiers are down there as well. They hide and wait until they pass by. Reza wants to leave in fear of his family but Scarlet begs for a few minutes. Leaving their hiding spot, they find the inscription Scarlet was looking forward. She begins to read it, amazed by what she finds. She then takes a chisel to it to Rezas surprise. Scarlet counters they are going to blow it up away. She knocks it away to find a bull statue, The Rose Key. It is covered in markings. Scarlet begins to read them as sirens wail. The blast is imminent. Reza tells her they need to leave NOW but Scarlet refuses saying this was what her father spent his entire life searching for. Reza runs and Scarlet says she will be right behind him. She quickly captures the rest of the statue on film and runs, as the blasting commences. She dodges debris all around her and nearly gets lost. Thankfully, she sees the entrance where she first went in and Reza drags her out.
Scarlet tells him she got the markings on film and now has the next step to finish her fathers work. Reza cautions her against looking for the Philosopher Stone. Her father looked for it, and His quest was a path to madness.
Cue Title Sequence.
Later, Scarlet is being interviewed by her cameraman Benjy (Edwin Hodge). She explains her mission to locate the Philosopher Stone, a famed item of supposed myth that could turn base metals into gold and grant who possessed it eternal life. Benjy asks about her father, and how his work possibly lead to his suicide. Scarlet is reluctant to talk about him and deflects from giving deep answers.
Scarlet and Benjy are in Paris, France. They go to the home of Nicolas Flamel, a famed alchemist who was purported to have the stone and used for immortality. They got to his crypt, and Scarlet explains that grave robbers open the caskets of Flamel and his wife hoping to find the stone, but both were empty of everything, including bodies, just adding to their myth. Scarlet says that the location of the stone was said to be hidden in code on the grave stone of Flamel but she is unable to translate the language but she knows someone who can.
Scarlet breaks into a church to Benjy's shock. Scarlet says she is looking for someone she knows, someone who breaks into places and fixes things. At the top of the church clock tower, they find George (Ben Feldman). George is less than happy to see her, telling Benjy the last time that he and Scarlet were together he got locked up in a prison in Turkey. Scarlet tells him she found The Rose Key, and needs him to translate for her. George realizes she went to Iran, alone, and is incredulous she put herself in that much danger. George finishes fixing the clock and they go outside to hear them ring for the first time in 284 years. George looks at Scarlet. "I'll help you translate but that's it", he says.
When night falls, they go back to Flamel's tomb and look at the grave marker. They try to translate several markings but get nowhere. Scarlet deduces they have to look at the back of the stone. They turn it over and find nothing. However, she thinks it is hidden via chemical reactions, so she mixes up some and lights it, revealing a message on it. They now have their next clue.
Benjy, Scarlet, and George look at a map trying to find a place to access where they need to go. They figure out that in the old days, people believe that hell was 741 feet down from Earth so they need to be halfway between Earth and Hell, underneath Flamel's tomb to find the stone. Scarlet realizes the catacombs are the only place low enough but Benjy notes that it is not far enough down. However, George remembers that in three spots around Paris, land cave-ins caused 100 feet of ground to collapse inward. One of those points is near Flamel's tomb. Scarlet realizes there must be a hidden catacomb in there.
Benjy and Scarlet go on a sanctioned catacomb tour. Scarlet points out to Benjy exactly where they would have to enter but it is too closed off for access normally. A teenage boy nearby tells her to find Papillion (François Civil) to be their guide. The Tour guide sees Benjy and Scarlet are trailing behind and urges them back to the group. When Scarlet looks back, the boy is gone.
Benjy, George and Scarlet go to a nightclub where Papillion is at. Benjy notices a strange girl that locks eyes with him intently. Scarlet tells Papillion about the hidden catacomb and though is unconvinced initially, is finally swayed when promised half of the treasure in the hidden catacomb. He tells them he will lead them.
The next day, the group gets ready their gear. Among the group is Papillion's friend Souxie (Marion Lambert) and Zed (Ali Marhyar). Benjy asks about Papillion's scars on his hand. Zed says they don't talk about that. As they prepare, George reminds Scarlet that he is not going with them. Still, Scarlet convinces him to at least follow them to the entrance.
When they get there, Benjy turns on cameras on each of their lights, so they can record everything that happens. George sees the small hole they are going through and balks at what they are doing. As they enter one by one, George is still vehemently against going. Suddenly, a police officer who had been following the group tackles Papillion and a scuffle begins. The group along with George flees into the tunnel in a panic. Papillion soon follows, and pops a smoke grenade so the cop will not follow them. Now free, they begin to go to work. Scarlet apologizes to George for him being there, but George doesn't want to hear it. He told her many times he didn't want to be here and yet he is.
The group begins to go down the catacombs. They stop at a split path. Papillion notices that the left path which they would have to swim to is a cool room but not the way they are going to. They take the right path and continue on. As they walk, they hear some kind of disturbing chanting. Looking through some openings in nearby rocks they see a group of women in some sort of ritual. Papillion notes they are plenty of crazy people that come down here. Benjy looks in and a woman gazes at him intently. He recognizes her from the club and is freaked out.
As they come to another crossroads, Papillion tells they have to take a path where they will have to crawl over a path of bones. Benjy says he will not do it, freaked out. Scarlet points out another path and says it will save the group hours. Papillion says absolutely not, as that is the bad path. Scarlett continues to argue but Papillion tells her he knows the catacombs better than she ever will. Furthermore, he, Zed, and Souxie had a friend named Mole who took that path out of eventual curiosity and they never saw him again. George talks to Scarlet and tells her that Papillion knows what he is doing and she can be a little more patient if it means keeping everyone safe.
The group moves through the path. However, Benjy gets stuck and begins to suffer claustrophobia. Scarlet works several minutes to calm him down, and he finally crawls through. However, his actions help cause a tunnel collapse and he barely makes it through alive.
When the six of them look around, it appears they are in the same place they just came from but there is no other way to keep going but the "bad" path Papillion refused to go through. The rest of the group overrules him, noting they have no other choice.
As they walk through, they see a graffiti symbol much like one Papillion tagged earlier. Scarlet confronts him over this, but he denies ever being in this part of the catacombs. Suddenly, they hear a ringing phone. George notes that they used to be some phone cables down in the catacombs but they were all taken out. As they continue to hear it, George sees a sign that confirms they are in the area where the ground collapse and a 100 people dropped to their deaths. Papillion confirms this and that when they went in to fix the problem, 50 more people disappeared.
As they continue to walk, they find an old piano, randomly sitting in a corner. Everyone thinks it is trippy. George says he used to have one that he and his brother Danny would play but the A4 key was broken. He begins to play a song but hits the A4 key to find it broken. George freaks out, asking Scarlet what is happening.
Scarlet continues to hear the phone ring and goes searching for it. She finds a rotary phone sitting on a table. She answers it and hears a disembodied voice on the other end. She asks who is there but gets no response. She slams the phone down in fright. The group then looks further down the path only to be confronted with Mole, Papillion's long thought dead friend. Mole asks if they are looking for a way out, and the group says yes. Mole tells them the only way out is down. He directs them to a well and they begin to set up to rappel down. As George is going down, Benjy preps to go down next. However, his rope breaks and he falls until he smashes into George. In the process, he hurts his hands badly, so Scarlett bandages them up.
When all six are down, they walk down a narrow corridor with an opening in the middle where water flows. Suddenly, the noise around them distorts, making it hard for them to hear, only to be replaced with loud, banging noises right after. In the confusion, one of their cameras catches the image of small child.
At the end of the path, there appears to be another dead end. However, George and Scarlet find some carvings in the stone and realize it is like an Egyptian tomb and they have press the right stone to get entrance. Using the inscriptions they have, they correctly guess the right stone and door opens.
The group enters and finds a well preserved corpse in Templar armor. Scarlet sees inscriptions on the wall that prove that her search is not a wild goose chase; the stone is real. On a hunch, she makes the group turns off their lights. Seeing a light coming from the floor, she discovers and underwater chasm that she crosses over. In it, she finds a treasure room and a wall with markings. The rest of the group come over and of course overjoyed despite the hardships that they are now rich.
Scarlet looks at the wall and relates a myth about the birth of the sun and his envy of his parents love. She finds the Philosopher stone and chips it out of the wall. She finds it funny that priceless artifact is right next to such to find treasure. Her face goes white. Its a trap! she screams too late. Papillion has just broken off the door of the treasure room, which causes a cave in to occur.
The group is all shook up but alive. They have to drag out Souxie from the rubble, and she got a messed up arm in the process. Scarlet uses shavings from the Philosopher Stone and heals her to the shock of the group. Realizing that Mole had apparently been killed in the cave in, they move on, trying to find a new way out.
Scarlet and George find a new opening and begin to crawl through. George finds an inscription and Scarlet translates it as Abandon all hope, ye who enter here which is supposedly what is inscribed at the gates of hell. Papillion is really freaked out by this point but once again, they have no choice but go through the path they have.
When they come out on the other side, they realize it looks like the room they just exited but everything is upside down and/or opposite. Papillion then sees the way they came in has disappeared completely. He asks Scarlet if they are dead in Hell. Scarlett says no.
Souxie sees Mole and is startled by him. She tries to go up to him to see if he is okay but he flips out, grabs her by the throat, and bashes her skull in on the ground to the horror of the group. As they go to help Souxie, Mole disappears. Papillion begs Scarlet to use the stone to heal Souxie but it doesn't work because she is already dead. Papillion is heartbroken and the group has to keep going. As they begin to walk, Scarlet sees a noose hanging only to look again and see that it is gone. The group realizes that everything they are experiencing now is a mirror image of what they have already done, and all they are doing is just going deeper down into the earth.
The group finds another well and rappel down. As Benjy gets ready to go down, he hears a baby cry. He turns around and yells if anyone is there. Looking again, the same woman that he had been seeing over and over screams and charges him. Startled, he falls down the hole without his harness and hits the ground, dead. Scarlet is absolutely horrified now that her expedition has now caused two deaths. George pulls her along, saying they need to keep moving.
They have crossed another path of bones. As George is going, he sees a reflection of Danny, his brother drowning. He screams, and tries to get to his brother through the bones. Scarlet has to calm him down, reminding him it isn't real, and why would Danny be here in the catacombs now. Crossing over the path, they see a light in the distance. Getting closer, they realize it is a fire. Turning the corner they see it is a car on fire, with a young man inside who turns and looks at him.
Papillion looks at the car in shock and screams: "NO! IT WASN'T MY FAULT!" (the boy is implied to be his brother or a close friend). Suddenly, an invisible force pulls Papillion towards the car. Scarlet and George try to hold him back but it is no use. Papillion is pulled into the flaming wreck, only for the flaming car to crumple up into a ball and disappear, leaving Papillion buried alive with his legs sticking out of the ground. Scarlet and George try to get him out only to realize it is too late for him. He's already dead.
Now the group only has Scarlet, George, and Zed. As they continue down the catacombs, they see a robed figure. Knowing it is nothing good, they hide behind a corner. Knowing they might be dead soon, George talks briefly to Scarlet. Whatever happens, the week in Turkey was the best week of my life, he tells her. Mine too, she replies.
The three of them look at the robed figure as he sits in a chair. He gets up after a minute and looks at them. The three run.
They take a breather on a wall that has stone figures built into the walls. The stone figures come to life and attack them, one biting George in the neck. Scarlet and Zed drag him away, destroying some of the stone figures in the process.
Scarlet tries to use the stone to heal George but it is not working. She realizes that now that reality is opposite, she never had the real stone. She has to go back to the wall where she found it, put it back and get the real stone. She tells Zed to watch George while she backtracks to the wall. Zed is afraid but Scarlet tells him if she doesn't go, George will die.
Scarlet backtracks through the catacombs. At the spot where water flowed through the floor, it has been replaced with blood and hands reach out, trying to grab her. Scarlet escapes their grasp. She comes across a hooded figure hanging from a rope. She believes it is a hallucination of her father, but when she takes the hood off, she finds herself, who screams at her. She runs off and finds the wall where she found the stone. She puts it back in place but isn't sure where the real stone is. Looking at the wall she finds a large, gold orb at the center. She wipes some dust off it and sees her reflection. It is not explicitly stated, but this reveals to her that her earlier words- "as I believe the world to be, so it is"- is literal in this mirrored world, that she has the power of the Philosopher's Stone.
On her way back to George, she sees a hallucination of her dead father, hanging from a noose. She gets up close and tells her father she's sorry she didn't take his call the night he killed himself. She didn't know he was that sick. His image disappears and she runs back to where George and Zed are, killing a few stone figures along the way.
Zed asks if she got the stone and Scarlet says yes. She then puts her hands on Georges neck and kisses him. When she pulls her hands away, his wounds are healed and he comes back to life. Seeing the stone figures chasing them, they continue deeper into the catacombs.
Scarlet finds yet another well down, but they know they will not have time to get down in a safe manner before the creatures get them. Scarlet says they will have to jump. Zed and George balk at doing that, noting they could die from a fall like that. However, Scarlet points out everything they have experienced and deduce if that they are actually in a circle of hell, they are being tormented for their guilt about past incidents. Scarlet is feeling guilty about her father's suicide, Zed had a child that he refused to acknowledge, and George's brother Danny drowned when he couldn't get back in time to save him. Scarlet says if they take a leap of faith and rectify their guilt, they have a chance. If they don't, they're dead anyway. George doesn't want to but Scarlet says she won't leave without him. The three hold hands and jump down the hole.
They land, bruised but alive. Looking around, Zed doesn't see any exits and freaks out that everything was for nothing. However, Scarlet thinks about the phrase that has defined much of their journey; "As Above, So Below" and figures out there is an exit on the floor. Scarlet and George discover a manhole and after figuring out how to get it open, climb through and the three finds themselves back on the streets of Paris. They quickly cover the manhole back up, sealing the entrance. Zed exhales in relief and shock while Scarlet and George silently embrace, all three traumatized by the ordeal.
The final scene is Scarlet's earlier interview with Benjy. She says some people think she is going after the Philosopher Stone for fame and fortune but it could not be further from the truth. Benjy asks if that is what she is really after, the truth. Scarlet confirms that is what she is truly after. "I want the truth", she says.