Internal dating: At the end of the case, Mulder writes his report, stating that the events took place between November 11th and November 13th 1994. They end up facing a month-long quarantine.
Pasadena, California. A volcano research centre picks up a distress signal from a team of scientists working at Mount Avalon. They also have a video sent by Firewalker, a robot which can go inside a volcano. This shows one of the party lying dead. As they watch a shadow passes across the picture, although nothing should be able to live in that heat.
Dr Adam Pierce, one of the scientists seen watching the video in the teaser, visits Mulder and Scully at the FBI HQ. He shows them a television news report about the Firewalker robot and its creator, Daniel Trepkos, who talks about this mission as being more as important as the mission to space - about revisiting the origin of the entire earth. Pierce tells them how the team sent a distress call, and shows them the video seen in the teaser. He says he used to be on the project but left six months ago, after personal differences with Trepkos, a genius. Despite his opinion of Trepkos, he's anxious that news of the problem doesn't get out, as it would if he goes through proper channels. "We're not exactly proper channels," Mulder says, smiling. Scully asks how soon they can get to Mount Avalon and is told they'll leave as soon as possible.
Mulder leans forward and says he doesn't think Scully should go. "I appreciate your concern," she says, "but I'm ready. I want to work." He says she should take some time off, but she says she's already lost too much time.
A helicopter takes them to Mount Avalon, then leaves them there. Pierce is anxious about the expensive satellite relay system and other instruments being damaged so stays outside to look at them. Mulder and Scully go inside the building.
There are no lights inside (of course) so they use their nice flashlights, which reveal that everywhere has been trashed. A man watches from the darkness, leaping out and attacking Mulder. They struggle, and Mulder wrestles the man to the ground. He says he's called Jason Ludwig and was only trying to protect himself. He thought Mulder was Trepkos.
Ludwig explains that Trepkos was always unstable - talkative one day, silent the next. He was a genius, seeing things normal people only dream of, then forget when they wake up. He introduces them to Peter Tanaka and Jesse O'Neil, the other team members, who are nervous and twitchy. Ludwig says everything that happened - including the other scientist's death- was due to Trepkos, and Jesse says he was sick, with a bipolar disorder. Trepkos was her thesis advisor, she says. Mulder finds Trepkos's notes, or what is left of them. Jesse says that he had tried to destroy all his notes. Mulder opens the notebooks, typically opening at exactly the right page to see "new life form" neatly written and underlined.
Mulder thinks the team is acting really oddly, but Scully thinks that's only to be expected, considering what's happened. Mulder claims that Ludwig knew he wasn't Trepkos when he attacked him, and there's something they're not telling them. He wants to ask Pierce's opinion, as he knew these people.
Outside in the woods, Pierce is attacked and killed by Trepkos. "No-one can leave?" Trepkos says.
At night, everyone searches the woods for Pierce and finally find his body.
Scully wants to leave and collect a larger party to deal with the situation, but Mulder wants to stay. He's been studying Trepkos's notes and reading about his claim that they found a new life form, silicon based, living deep within the volcano. Scully says that all life is based on carbon, but Mulder argues that silicon-based life forms is the next life from to be discovered - a holy grail of science. Scully says this is just science fiction, not science, and that Trepkos was delusional. She says that the while team have post traumatic stress disorder and should be evacuated.
Scully talks to Jesse, who tells her that Trepkos became withdrawn after the first descent into the volcano. He stopped taking his pills, saying they were polluting his brain and that she was polluting his body. Scully asks her what she's afraid of, and she says "Daniel." She only came because of him. He'd promised it would be a life-changing adventure, but now she only wants to get out, "anywhere but here."
Mulder listens to a recording of Trepkos's voice, saying how he's sleepless with wondering about this new lifeform - wondering if he's lost all perspective, "if my intense desire to find the truth hasn't in fact eclipsed the truth itself." He says his mind is a tangled knot he can't untie, and he daily wishes he could sever it completely - to stop this descent.... The tape stops, and then there is a quake.
Tanaka is feverish, but resists when Mulder says he'll ask Scully to treat him. Then he collapses. Scully does look at him after all, and says he needs a hospital, though she can't tell what's wrong with him. They call for a helicopter to evacuate them and carry the stretcher outside. As they carry him, Tanaka's throat convulses and he breaks free, running out into the woods. A nice chase with flashing torches ensues, before Tanaka falls into a hollow. Ludwig wants to go down, but Mulder restrains him. and they watch as something rather nasty bursts out of his throat.
Scully studies the object and says it looks like a fungus of some sort. A spore grew inside him until it burst out of him, too big to stay inside. There was sand in his lungs, which Mulder thinks indicates a silicon based life form. Ludwig objects, saying this doesn't exist, but Scully says that perhaps it does, though still says they have to study it more before pronouncing. Mulder says Trepkos discovered the spore but didn't tell anyone, and Scully thinks the spore could explain his dementia. No-one can leave, Scully says, until they determine how infectious they are. They voluntarily quarantine themselves.
Mulder says he has to find Trepkos, even though he could well be dangerous. Trepkos has made an incredible discovery, he tells her, and he has to find out what it is. Scully wants to come with him, but he refuses. "Look, I know what you're thinking," Scully says, "but you've got to get past that - we both do. I'm back, and I'm not going anywhere." Mulder points out that she has to finish the autopsy anyway - that this is essential to getting them out of this mess. "I'm counting on you," he says, hand on her shoulder.
Mulder asks Ludwig to tell him how to get to the site of the strange images seen in the Firewalker video. He offers to guide him, saying he won't get there without him. He wants to lead Mulder to Trepkos so Mulder will kill him.
In the caverns, Ludwig is hit by a bolt of flame, fired by Trepkos, who makes Mulder hand over his gun. Trepkos burns Ludwig's body, saying "it's not him I'm trying to kill."
Scully attempts to culture the spore in numerous different ways, but can't grow the fungus. She decides they are only active if they re inhaled or ingested by the host immediately, but die very quickly. She shouts through Jesse's door, telling her that they are probably all in the clear, but inside Jesse's throat is convulsing.
Mulder talks to Trepkos, who says "the truth is an elephant described by three blind men" - different to everyone. He says there are some truths better left buried. Mulder says he came here purely to find out what killed the scientist, but Trepkos seems to understand him, and says he knows he came seeking "some penetrating answer". "If you found that answer," he asks. "What would you do with it?"
Trepkos explains that Ericksen, the first dead scientist, found the spores in a rock. He himself was so immersed in the work, alone in the lab for three days, that he failed to notice what was happening to those around him. By the time he noticed they were all affected it was too late. He killed Pierce because he wants to keep the contagion confined to s small area. Mulder wants to go to check up on Scully, whom he calls "a colleague - a friend". Trepkos points a gun at his head, but Mulder says he'll go back to her, regardless.
Scully is working on the tests when the lights go out. Exploring with a torch, she finds Jesse, covered with sweat and her throat convulsing. Jesse handcuffs herself to Scully. Scully tries in vain to hack through the chain, as the thins begins to push itself out of Jesse's throat, but in the end managed to push Jesse through a door, and keep herself on the other side of it. The spores explode over the glass, and Scully sinks to the floor, exhausted.
Mulder rushes in, shouting. "I'm okay, I'm okay," she says, looking far from okay. Mulder touches her cheek, and gently helps her up.
Trepkos comes in and sees Jesse lying dead. "I told her it would change her life," he says, visibly moved.
Mulder calls for evacuation, saying that only he and Scully are left. Scully is horrified, asking why he's letting Trepkos escape. "It's over, Scully," Mulder says.
Scully and Mulder enter a month long quarantine. The military biohazard corps have confiscated all their notes, and there are no plans to explore the other volcanoes.
As Mulder's report continues, as voice-over, Trepkos carries Jesse into the volcano, and Mulder lies on his report about what happened at the end, claiming that he doesn't know what happened to the two of them. His report dates the events of the case as being between 11 and 13 November 1994, and says, "mine stands as the only record."
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