The episode starts out, in the teaser, with a voice over from Mulder telling what the Syndicate has been doing. (Kind of like a recap)
Flashbacks are shown.
In Mulder's apartment, before Mulder can make the decision of shooting Cassandra, the CDC, headed by Diana Fowley, comes in to put Mulder and Scully in quarantine.
Mulder and Scully are put into a decontamination shower. They are in separate stalls but they can see over the low walls. Mulder and Scully both appear to take a peek!;-)
Diana apologizes to Mulder and Scully but says that Cassandra could have infected them with a contagion.
Mulder and Scully's clothes have been destroyed. Scully takes a gray shirt out of the locker.
SCULLY: They burned our clothes.
MULDER: Hey, I heard gray is the new black.
Mulder tells Scully that Cassandra knows what is happening, that she knew she needed to be killed, which was why she came to his apartment. She is the one.
EAST 46TH STREET
NEW YORK CITY
The Syndicate are having a meeting. It Cassandra is not destroyed, colonization will begin. CSM tells them to let it begin.
FORT MARLENE
DECONTAMINATION FACILITY
9:02 p.m.
Mulder tries to flag down a nurse to get another pair of shoes, because his are two sizes too small. Apparently the rest of his suit is too - the pant legs and arm sleeves are definitely too short.
In the hospital, Mulder meets up with Marita, who looks really sick. She explains that she has been experimented and tested on - but not to be made a hybrid. They were using her as a guinea pig to test the vaccine, once she had been infected with the oil.
At the Lone Gunmen's place Frohike opens the nine locks on the door to let Mulder in.
MULDER: The latest in home security.
FROHIKE: Hey, you get through this you gotta come through me.
Mulder tells Frohike that Scully had called him and said it was urgent.
Scully comes over and tells Mulder to hear her out before he says anything. She had them pull up information on Diana Fowley. Mulder says that he knows her, she doesn't. Scully tells him that he did, but that he doesn't anymore. It seems Diana had been travelling all over Europe and talking to members of MUFON who are abductees. She had been taking trips almost weekly to Tunisia. She went to every MUFON chapter to collect data on female abductees.
Mulder tells her that she was only collecting data. Scully cuts in, saying that Diana could also be hiding data. Mulder tells her she's reaching.
Scully tells him that when she was abducted and had the implant put in her neck, she had come upon the MUFON group who had had the same experiences. Mulder asks if she thinks Diana is monitoring them.
Scully tells him that he keeps saying that Cassandra is the one, but who is watching her? She tells him that she can prove or disprove what he's saying, but not when Fowley is keeping them from even seeing Cassandra. There is no information whatsoever on Fowley that she could find. Scully asks why Fowley suddenly comes into his life when he's closer to the truth than he's ever been. He had asked her to trust no one, but he is trusting Diana on simple faith. He tells Scully it is because she has given him no reason to do otherwise. Scully says then that she can't help him anymore.
MULDER: Scully, you're making this personal.
SCULLY: Because it is personal, Mulder. Because without the FBI, personal interest is all that I have. And if you take that away then there is no reason for me to continue.
THE WATERGATE APARTMENTS
7:04 p.m.
Mulder goes into Fowley's apartment to snoop around for any incriminating information. In the process he find's her underwear drawer, but passes it up and continues to look.
Suddenly he comes across CSM.
MULDER: Sorry. Nobody home. What are you doin' here?
CSM: The door was open; I came in.
MULDER: Interesting company you keep.
CSM: No more interesting than your apparent lingerie fetish.
Mulder pushes CSM into the room into a chair and points his gun at him.
MULDER: You feelin' smug, C.G.B.? Yeah, I know your name. I know your game, and I got nothin' to lose.
CSM: I remember looking over a gun barrel at you once before, Agent Mulder. You couldn't pull the trigger then, what makes you think you can do it now?
Mulder talks to CSM who explains what has been going on since Roswell. The Syndicate had a majority vote to side with the aliens. Bill Mulder was against this. They became their own government agency. They had no choice but to sacrifice their loved ones, in hope that they would be saved and returned. Bill Mulder did not accept this. Bill Mulder was the only one who didn't see their survival as the ultimate ideology.
Mulder tells him that his sister wasn't abducted at any base, but right in front of him.
CSM tells him that his sister was abducted from her home, because his father was late to understand the necessity that he had to give up a child to the alien colonists. They had insisted on it.
CSM: It was the only way they would give us the one thing that we needed. The one thing without which we could not proceed. (alien fetus is shown) See, the alien fetus would give us the alien geno - the DNA with which we could make a human hybrid. A new race, Agent Mulder. An alien-human hybrid - who could survive the holocaust. So YOU could survive and live to see your sister.
Mulder guesses that they have succeeded. CSM says that they have, in spite of themselves. They were working on a vaccine until the rebels came and destroyed their plans. It had been Mulder's father's idea to make the vaccine, to save the world. But now, it was too late. Colonization will begin. A sequence of events will occur and a state of emergency will be declared, because of a massive outbreak of an alien virus by bees - and take over will begin.
If Cassandra were to survive and the aliens found out, colonization would began, thus why it is imperative that she must be killed. The rebels are trying to stop this.
CSM gives Mulder a piece of paper. Even though Mulder waves his gun around, telling CSM to stop it, or he will, CSM tells Mulder that they will survive as the rest of the world dies, or he can die in vain with the rest of the world.
EAST 40TH STREET
NEW YORK CITY
Krycek comes into the office to see Spender. He asks him if he's looking for his father, because he's not there. He tells Spender that he's not coming back, everyone went to West Virginia with the other members of the Syndicate. They will be transported by the colonists, and they will begin medical preparations to receive the hybrid genes. Except for his father - he went to get Cassandra. Spender tells him that he won't be able to find her, because he has her safe. Krycek says he's already with the doctors looking at her. She's probably being prepared as they speak.
Cassandra is being injected and held down by doctors. She is screaming at them when CSM comes in. He came to kill her, but he can't.
When Diana comes back to her apartment, where Mulder had snooped for evidence of her betrayal when he had met with CSM, he tells her that he didn't find anything. She takes the paper from him. It's an address of where he can be saved. Fowley kisses Mulder and hugs him, but he doesn't really respond. It's kind of like a 'good bye.'
PORT MARLENE
10:13 p.m.
Spender goes into his mother's room to see her, but she is not there. He finds Marita who is begging for his help. She tells him that everyone left and is not coming back for her. She tells him she knows where his mother is, and how she was taken.
MARITA: You've got to trust me, Jeffery.
A man is taking out an alien fetus (like the one seen in "The Erlenmeyer Flask") out of a container of liquid Nitrogen. Suddenly a nurse, the one who had ignored Mulder, is standing in the doorway. The man tells her she has to leave, but she doesn't. She comes over and kills the man. Another man sees this, but obviously a rebel, does nothing.
They are on their way to get Scully when she calls. Spender had told her he knows where his mother is. Mulder tells Fowley to go ahead to the base, and he heads off to get Scully.
Mulder and Scully find what they are looking for. Tanker trucks. (These are big white tanker trucks and music from the movie is playing in the background - the part that is played when Mulder and Scully were chasing the BIG WHITE TANKER TRUCKS!) Mulder and Scully shoot at the truck.
EL RICO AIR FORCE BASE
11:21 p.m.
At the air force base the men from the Syndicate and their families gather.
Mulder and Scully find Skinner and ask him for his help, telling him that there could be mass panic - at El Rico Air Force Base.
CSM arrives with Cassandra. A man from the Syndicate wants to know why they were late. CSM tells him that they were shot at, but that he doesn't know by whom. CSM says that they have people missing, and asks where Alex Krycek is.
Krycek goes into the storage room to get the alien fetus. He finds the doctor frozen from the liquid Nitrogen. He goes over to the canister and pulls the case that holds the fetus out - it's empty; the alien fetus is gone.
Spender yells to Krycek when he sees him. Spender tells him that he needs his help. The hospital has security and they won't recognize his authority to remove a patient. Krycek sees Marita. Spender tells him that his father (CSM) did this (the experiments) to her, and that she wants to tell her story.
KRYCEK: You don't get it, do you? It's all goin' to hell. The rebels are gonna win.
Krycek looks to Marita and tells her that they took it. Spender wants to know what he is talking about.
Before Mulder, Scully, and Skinner can make it, Fowley, who had went on ahead to the base, goes with Cancerman to her car and they leave.
Faceless rebels come into the base and surround all of the Syndicate, as well as their families who had been going to be saved.
In Kersh's office, Kersh is looking at photos of all the burnt victims from the base. It seems they were all torched. Mulder, Scully, Skinner, and Spender are there. Kersh tells him he's sorry about his mother. Spender says that's not why he came. He says that he is responsible for the deaths of the people, at least he didn't try to prevent them. Kersh then, wants an explanation. Spender tells him that Mulder can explain what happened, and probably Scully as well, to an extent. They might even have prevented what happened. Kersh yells at Spender and says that Mulder and Scully have been relieved of their positions at the FBI. Spender tells him that that was his (Spender's) doing, and that it was his mistake. Kersh starts to say something, but Spender interrupts him.
SPENDER: I'd ask, sir, before you tell me it's not my business, that you do everything you can to get them back on the X-Files. Far worse can happen, and will.
Kersh yells at Spender, but he leaves, saying he is going to pack up his office.
Kersh asks Mulder why he never told him they had this information.
KERSH: You have answers now? Why didn't I hear about those answers before?!
MULDER: I've had answers for years.
KERSH: Then why didn't we hear about them?!
MULDER: Nobody ever listened.
KERSH: Who burned those people?
MULDER: They burned themselves, with a choice made long ago by a conspiracy of men, who thought they could sleep with the enemy. Only to awaken another enemy.
KERSH: What the hell does that mean?!
MULDER: It means the future is here, and all bets are off.
KERSH: Agent Scully, make some sense.
SCULLY: Sir, I wouldn't bet against him.
Spender finds CSM in his office and tells him to get out. CSM is disappointed in his son. He takes a picture off of Jeffery's desk. It is the same one as Scully had before of Young CSM and Bill Mulder. He tells him that they are two fathers, that this meant something. Bill Mulder was a good man and a friend of his, who betrayed him in the end. Spender tells that he knows enough about him (CSM) to hate him. CSM replies that Jeffery's mother was right. He came hoping otherwise. He had hoped that his son might live on to honor him, like Bill Mulder's son. CSM raises his gun to Spender.
A shot is fired as the camera pans away.