Detailed summary: Part 1: The Needs of the Many After the events of "Jump the Shark," the Lone Gunmen wake in a government facility realizing that they are not, in fact, dead. A mysterious "doctor" has come to help them--it is Deputy Director Kersh. Once they have safely escaped from the facility, Kersh explains as his motive that you can't be a player in this game without controlling part of the board, and he got tired of being someone else's pawn. Kersh drops the trio off with only some cash and new IDs, telling them not to resurface. Instead, they go to a bus station in Baltimore and retrieve their emergency kit: disguises and false IDs tucked away for just such an occasion. Frohike and Langly decide to go look for Mulder, who has dropped out of sight since "Trust No 1," but Byers says he needs to go somewhere else first: to find Susanne Modeski. They say their goodbyes. After a couple of dead ends, Frohike and Langly go to New Mexico to see if the Hosteens have any news of Mulder. They get a ride with a young Navajo man who seems to know a little too much but won't share any details. The young man takes them to a trailer on the outskirts of the town, and Mulder emerges. The three have a lot of catching up to do. * * * * * Part 2: Father's Day While Mulder, Frohike, and Langly are playing cards, Gibson (who has been hiding out on the reservation with Mulder) suddenly shows up and announces his premonition that William is in danger. Mulder wants to go after him, but the guys determine it's too risky, so Frohike and Langly volunteer to go instead. They pay a surprise visit to Skinner, who is a little annoyed that they are alive after he went to so much trouble for them to be buried at Arlington. He tells the pair of the recent events (from "William") and of Scully's decision to give her son up for adoption. Frohike and Langly formulate a plan and contact Mulder, but they all agree not to inform Scully. Skinner helps Scully hand over William in the secretive adoption, and the boy is given over to the Van de Kamps. Only, the "Van de Kamps" are really Joe Fuhrman and his wife, old friends of Frohike. Once the social worker is out of sight, the couple pass William over to Frohike and Langly, who finally reunite the boy with Mulder. In a final, private moment, Mulder rocks his son to sleep and promises to take good care of him for Scully. * * * * * Part 3: Triangle of Love Skinner stops by Quantico to see how Scully is doing, only to find her looking weak and pale. He invites her to dinner and impulsively tells her they need to go somewhere to talk so he can share news of Mulder. Skinner contacts Frohike and Langly, and they relay to Mulder that Scully isn't doing so well. They decide that maybe it's time for Scully to come join them. After she's had time to consider this option, Scully decides to fake her own death in order to go join her family, and she asks Skinner to help. In an elaborate and risky plan, she uses the rumor that she and Skinner have been seeing each other to fake her suicide at his hunting cabin. In fact, she has taken a drug that will repress her breathing and heart rate to undetectable levels. Skinner must report her death so that a death certificate can be issued, but he must also ensure that no autopsy is performed and the antidote is administered in time. Skinner cuts it close, but he does manage to revive her before the clock runs out. Fulfilling one last promise to her, Skinner must deliver news of Scully's death to her mother, along with an urn containing her "ashes." But he holds back one thing--the vial containing Scully's microchip. Meanwhile, Scully has been reunited with Mulder and William, and the three finally get to be a family. * * * * * Part 4: In Memoriam As a brief interlude in the action, Skinner pays a visit to Mrs. Scully at her request. She is packing up to move to the West Coast, and she ran across something she wants to give him. It is Dana's pin from the Academy, for placing first in her class. Mrs. Scully wants Skinner to have it because she's heard the rumors about him and her daughter, but also because she believes he knows more than he's letting on about William and Mulder, and she thinks he might be able to pass this on to William someday. Skinner reveals nothing, but he does tell her to contact him if she ever needs anything. She regretfully packs away a picture of Dana, lamenting the loss of yet another family member. * * * * * Part 5: Touchstone A couple snuggle in bed together, deciding that it's time to come out of hiding and return to the fray: it is Byers and Susanne. Back in New Mexico, Gibson and William are playing together. Gibson realizes that someone is coming, just as Mulder rushes in to ask who it is, but Gibson knows it is a friend. Byers has found them. Now that he has rejoined his bachelor buddies, things are a little awkward with the addition of Susanne to the equation. However, the couple has not arrived empty-handed; Susanne has been busy collecting data about government projects, and she knows a lot about chloramine (as explained to Scully in "Nothing Important Happened Today"). Susanne tells them that in areas where the water has tested positive for a particular strain of altered chloramine, there is a rise in infertility rates and reproductive intervention. The chloramine is therefore either being used to produce mutated eggs (to create Super Soldiers), or the women are being driven to fertility doctors, who can implant engineered embryos. They also think that magnetite may play a part in the whole scheme, but they aren't sure yet what that might be. Later, Susanne reveals to Scully that she might be pregnant. She knows that Byers will be happy about it, but he'll also want to get married. Legally, this is impossible, since they are all living in hiding. But there is still a way for them to get married. In a Navajo ceremony, Byers and Susanne promise their commitment to each other, as do Mulder and Scully. Afterward, an old woman, Albert Hosteen's mother, gives Susanne a necklace "for babies" (as she says in a heavy Navajo accent). They assume it is a fertility gift for a new bride, but no one mentions the fact that only Susanne received such a necklace. * * * * * Part 6: Truth or Consequences Scully and Susanne have been working to find an additive that will counteract the modified chloramine, with the intent of disseminating it in water supplies all over the country, although it is still uncertain how exactly they will spread the additive once they develop it. In the meantime, Mulder is getting restless, feeling like he is little more than a babysitter. He discloses to Byers that he has had visions of Albert Hosteen, who has told him about a man living in the distant hills who can tell him about the Truth. Mulder hands William to Byers and takes off to find this man in the hills. He follows a column of smoke to the ruins of an ancient hillside pueblo. Inside, he finds someone he never expected to see again: the Cigarette-Smoking Man. CSM tells Mulder that these hills are the only place people will be safe when the end comes, and the Anasazi Indians knew that. Mulder puts the pieces together that the hills are full of magnetite. CSM offers Mulder a key card that will lead him to the Truth. Mulder rejects the card, so CSM tells him that the date has already been set: December 22, 2012. Mulder sets the cave ablaze and watches the fire from the other side of the canyon. Scully finds Mulder here, and he explains what happened, including showing her the key card. When the rest of the group comes to check out the smoldering ruins, they find a tunnel at the back of the cave, leading to a water source and a possible way out. Frohike and Langly have been off visiting Joe Fuhrman and checking out the self-sufficient doomsday compound that he's purchased. As they're telling the group about their visit, Mulder pulls away, and Scully detects he's holding something back. He finally admits to everyone that they're working against a deadline, that the date for invasion has been set. But, rather than discouraging them, the news only makes the group more determined to fight back. * * * * * Part 7: There Comes a Time Skinner is called to a late-night meeting with the X-Files agents at a nondescript diner. Doggett and Reyes have anonymously received a list of ten names, with Agent Crane at the top. They are guessing that all ten are Super Soldiers placed within the FBI. Skinner recognizes that all ten have recently been promoted, but he tells the agents not to pursue this further because of the risks to their jobs and possibly their lives. However, Skinner pockets the list and does some investigating of his own. He discovers that the personnel files for all ten names are in the possession of Deputy Director Kersh, so Skinner takes the risk of breaking into Kersh's office. He finds Kersh waiting in the dark. They have a cryptic conversation, and Kersh warns Skinner to watch his back, but he doesn't stop Skinner from leaving. Skinner is apprehensive of the consequences. Later in the week, Skinner is returning home from the gym and needs to go back to his car. He finds a man there, tampering with something under the hood. Skinner wrestles the man unconscious and makes a decision. He puts the man in his car with his own ID, then triggers the car bomb and takes off. Back in New Mexico, Mulder and Scully are saddened over the news of Skinner's death. While they are waiting for Michael Hosteen to return from a council meeting with news of whether they have permission to build at the pueblo ruins, an unfamiliar man drives up. He removes his disguise, and they recognize Skinner. Michael Hosteen returns and tells Mulder that the Navajo will look the other way if they wish to build at the pueblo. * * * * * Part 8: Two of a Kind In a brief story, Gibson and William are playing in the trailer while some of the adults discuss the latest on the chloramine project and construction at the ruins. Gibson narrates what it is like to have open access to others' thoughts. He and William escape to the bedroom, where things are quieter, as more people arrive at the trailer. Gibson is trying to teach William how to say certain words--only, William's mouth isn't moving as he's saying them. Gibson wants William to learn to speak out loud, not just in his head, so the adults won't know their secret. Gibson knows what it's like to be special, and he doesn't want William to be treated the same way. * * * * * Part 9: Of Miracles and Magnetite Construction is progressing, and the cave at the ruins has been converted into a whitewashed room that will potentially serve as a lab, although Scully and Susanne aren't so sure about that. While discussing the possibility, Scully gets a nosebleed. They have been talking about Susanne's pregnancy, so Scully suggests the two of them sneak off to the city to visit a larger medical facility. When they return, they each have news to share, but Scully isn't eager to make hers public: Susanne is expecting twins, and Scully has found evidence that her tumor returned. Scully can no longer hide the news when she gets a nosebleed right in front of Mulder. He follows her into the bathroom to confront her about it. Scully admits that she removed the microchip so she couldn't be tracked to New Mexico. Skinner interrupts to share his own news, that he didn't dispose of the chip with her "ashes" as she had asked, and that he has it hidden away and can retrieve it. Mulder is relieved but not happy with Scully for lying to him. The group talks more about the technology of Scully's chip, and Susanne shares what she understands of how it works and how they can retrieve it without being tracked. Susanne believes that Scully's chip may be an earlier prototype for the same type of nanotechnology (like what was used in Skinner) that is part of the Super Soldier program. The chip emits a signal like a radio, but only when connected to a power source, such as the human body. Once the chip is reimplanted, it can send a signal, so they need to block it. They realize that the magnetite in the hills might do the trick, so they come up with a plan for Scully to live in the remodeled cave once Skinner has retrieved the chip. While Skinner is gone, Scully decorates the trailer for Christmas, not knowing whether she'll still be living there when the holiday arrives or whether Mulder might come with her to the cave. The tension remains thick between the two of them, even after Scully moves into the cave, alone. Her time there is lonely, which she explains to Joe's wife, Pat, who contributes some friendly meddling, telling Scully that Mulder will come around eventually. Since Scully can't leave to celebrate with the whole group, they bring Christmas to her and have a Christmas Eve party at the pueblo. Mulder arrives late and is distant, but as everyone is leaving, he hands off William to a babysitter for the night and surprises Scully with his offer to stay the night, which she gladly accepts. * * * * * Part 10: Precious Gems Frohike and Langly have found a way for Scully to leave the cave by crafting her a necklace of magnetite beads, painted turquoise to look Navajo, that block out the transmissions sent by her chip. But in order for it to work, she can never take it off. Since the necklace is magnetic, Scully can no longer wear her cross, so she asks Mulder to keep it safe for her. He agrees, and she fastens it around his neck. Back at the trailer, Mulder is cleaning up in the kitchen while William is napping and Scully is at the store. A car drives up. Joe and Pat Fuhrman have returned from Montana, along with "the boys," Cody and Hank (the two men who are helping with the construction), but they also have a guest in tow: Ruby Morris (from "Conduit"). Ruby has been looking for Mulder. She shares about her abduction experience, and her healing while staying with Absalom's cult. She believes Mulder can help the abductees. Scully returns from the store, surprised to see Ruby. Ruby has a strange reaction to Scully's handshake, but Mulder guesses it was an electric shock from the cold, dry January weather. Ruby continues to act oddly while Scully puts the groceries away. Suddenly, William starts to scream, and Gibson rushes in the front door. He announces that Ruby is a Super Soldier. She says she has come for William. Mulder keeps Ruby occupied in conversation while Gibson sneaks up behind her and drops a magnetite necklace over her head. The beads slow her down, but no more than that. Mulder drops her with a bullet. Later, Ruby is restrained in Skinner's camper, while Gibson returns with Frohike and Langly. Scully has asked Joe and Pat to take William to the pueblo and protect him. Mulder and Scully try to interrogate Ruby, only to learn that the magnetite has suppressed her connection with the Super Soldier "collective," similar to its function with Scully's chip. The real Ruby is starting to emerge and wants them to help her if they can. Scully and Susanne set up a lab at the pueblo to find an antidote for Ruby, while the rest of the men step up the renovations on the pueblo to create suitable dwellings. Susanne and Scully have found Ruby's blood to be full of nanites made of magnetite. They hypothesize that carbon nanites, such as in Skinner's blood, are the best weapon against the magnetite nanites since they can rapidly multiply. However, they don't have the knowledge or technology to make this work. Instead, they are creating a ferrofluid--an oil full of magnetite particles--which will hopefully bond with the magnetite nanites in Ruby's blood (like iron filings drawn to magnets) and render them inert. While they work in the lab, Scully secretly tests some of William's blood for nanites, but she is relieved to see that his blood is normal. When the fluid is ready, Mulder and Scully return to the camper to try it on Ruby. They tell her there are no guarantees, but she says she would be better off dead than to live as a Super Soldier. The injection at first seems to have no effect, but then there is a violent reaction. Ruby turns ashen and disintegrates before their eyes. The group gives Ruby a burial at the base of a hillside near the pueblo. They have created an impromptu campsite outside the ruins with Mulder and Scully's trailer, Skinner's camper, and the Fuhrmans' motorhome. Frohike and Langly have moved into a completed room in the pueblo. As the group returns from the funeral, Byers and Susanne express their doubts whether it is safe for them all to stay here. Mulder assures them he believes this is the safest place for them all to be, because there is a presence watching over them. He also thinks Byers, Susanne, and Gibson are safe in town with the Hosteens because of Albert's spirit. They all agree to stay here together. Later that night, Mulder wakes alone and finds Scully in the living room rocking William. They share their doubts and fears about why the Super Soldiers would want William and what kind of future he has. They are resolved to do whatever is necessary to keep him safe. * * * * * Part 11: Great Minds Agent Crane arrives at the reservation and finds Mulder, who is traveling from a Blessing Way ceremony for the ill Michael Hosteen to meet up with Scully. Mulder is preoccupied with the medicine man's comment that there are evil spirits present. Scully and William are with Susanne at the hogan on the Hosteen property. The women are discussing the force field that Byers and the guys have gone to purchase to protect their complex at the pueblo. Mulder arrives, not realizing that Crane has followed him there. While Mulder goes into the hogan, Crane heads for the house, where Gibson is alone. In the hogan, the adults are surprised when William says his first words: "Hep Gips." Mulder runs for the house, and as Scully grabs her gun to follow, Susanne gives her a syringe with the magnetite fluid they had injected into Ruby. Mulder shoots Crane with a magnetite bullet, which has some effect, but when Scully injects him, Crane disintegrates. Once the danger has passed and while they await the return of the Gunmen, Mulder discusses with Gibson and Scully why Crane came after Gibson and how William is like Gibson. They determine that William is not a Super Soldier, thanks to the injection by Jeffrey Spender, but that like Gibson, his junk DNA is active, allowing him to read minds, which represents the next step in human evolution. If any of the children affected by the chloramine, as William once was, were to also have their junk DNA turned on, the Super Soldiers wouldn't be able to control them, which is why children like Gibson and William are a threat and now targeted by the Super Soldiers. Mulder fears that with the attacks by Ruby and Agent Crane, the danger from the Super Soldiers has only just begun. The whole group moves into the new complex at the pueblo, which includes a two-story dormitory and a three-story abode structure with a common room, bathroom, and kitchen/storage facilities. They set up the force field, which uses antiparticle technology, and test it out. Since the force field can annihilate anything that crosses its field, they decide to build a defensive wall from the leftover adobe bricks and set up the force field close to the wall, to avoid the danger of any of them or their children accidentally walking through the field. When they set up the force field to cover the length of their compound, at first it doesn't have enough power to work. They are distracted from working on it when the medicine man, at Mulder's request, has stopped by to do a blessing ceremony over their complex. During the blessing, the medicine man stops abruptly and walks to the far end of their compound, to the ruins of an adobe building that they are using for a storage space. At his instruction, they move a pile of rubble and discover an opening leading to a large cave, which has a large piles of bones that apparently belonged to the Anasazi. The medicine man tells them that the dead must be buried, meaning that they must carry off the bones to a remote location and take care that the spirits of the dead do not follow them home. When Mulder returns from this task, he and Scully discuss the fate of their son as Scully still struggles to accept his new ability. As the final part of the house blessing, the entire group comes together for a communal meal.