Three Words - Recap
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A man climbs the gates of the White House and jumps onto the front lawn then runs toward the front doors. Stopped by Secret Service. As they're taking him down, he yells that he has to tell the President something, that aliens are taking over the United States. He has a gun and a shot rings out. The agents say he accidentally shot himself. The man hands one of the agents a disk with "Fight the Future" written on it.
Mulder is sitting in his hospital room. He's having flashbacks of the painful experiments that were done on him. Scully comes in with a doctor. They tell him that the virus is gone from his body, that his body is healing itself, and that he is now in perfect health.
Mulder and Scully return to Mulder's apartment. Scully tries to tell him what it was like when he was gone, how glad she is to have him back. He is less than receptive and tells her that he's confused as to how he fits into things now.
At a correctional facility in West Virginia, Absalom is handed a newspaper article that reports the death of the census worker killed in front of the White House.
Skinner and Doggett are called into Kersh's office. Earlier that day, Scully had submitted an application for Mulder to be reinstated to the X-Files. Kersh points out the increased success rate of the X-Files since Doggett was assigned to it. He asks Doggett to tell Mulder that the FBI isn't for "personal crusades," and that Mulder's application is denied.
Back in Mulder's apartment, Scully and Skinner break the news. Mulder finds out that Doggett has been Scully's partner the last few months. He tries to make some cracks, but Scully sticks up for Doggett. Mulder goes to get dressed: "For the first time, I feel like getting back to work." Scully and Skinner exchange a look.
Absalom is with a prison crew doing construction on rural road. He manages to escape.
When Doggett gets home that evening, Absalom is there with a gun. Abs checks Doggett's neck for implants to "make sure that you're still you." Shows Doggett the newspaper article. He says that they will kill him next. Abs says Doggett will have to come with him, Doggett will have to spread the word - that the invasion has begun.
Scully calls Doggett while Skinner briefs a group of agents on Absalom and his escape. After the briefing, Skinner asks Scully where Doggett is. She says she can't get a hold of him. Then Mulder sends her a text message: "Where is everybody? Come on down! Mulder."
Mulder has made himself comfortable in the basement office. He found an old class picture of Absalom on Doggett's desk. Points out to Skinner and Scully that the man shot at the White House is also in the picture. Names the man (Howard Salt) and says that he was a multiple abductee, and was killed for what he knew. Also says that he thinks Salt was bringing someTHING to the President. Scully and Skinner are skeptical. Mulder makes another dig on Doggett.
Absalom is taping a gun to Doggett's bare back.
Mulder is being usual snarky self in the FBI Evidence Room, going through Howard Salt's personal effects. Still making digs at Scully for having a different partner. Finds something on Salt's laptop that's been encrypted. Takes the hard drive.
Federal Statistics Center: see Abs leading Doggett into the building. The guard that lets them in notices the gun at Doggett's back and sets off silent alarm. Abs says he needs access to wherever they compile all the data for the US Census. Says that proof of the invasion is in the census data. Doggett and Abs are confronted with guards. Abs is shot dead.
In Skinner's office, Doggett tells Skinner what Abs told him. Mulder walks in and immediately shoves Doggett, accusing him of hiding the truth, of getting Absalom killed. Skinner tries to make up excuses for Mulder's behavior, but Doggett just leaves.
At Scully's apartment, the Lone Gunmen are there going through Salt's hard drive. Found a series of file directories from the US Census Bureau. Found that 15 minutes after Salt was killed, firewalls went up on every databank in the facility. Langly can't get past it without a password. And even with the password, you'd have to break into the FSC to get into the databank. And Mulder continues to be an ass by accusing the Lone Gunmen of siding with Scully.
Doggett secretly meets with Rohrer to find out what the hell is going on - why Abs was killed so point blank at the facility, what is being hidden. Rohrer tells him to watch his back - that the men he's dealing with shoot first and ask questions later. Doggett says he knows that. Doggett says, "What don't I know?" Rohrer says, "Three little words."
Doggett meets Scully outside Mulder's apartment. Tells her that Salt had a disk he wanted to give to the President, and that it came with a passcode: Fight the Future. Asks Scully to pass it along to Mulder.
Scully goes back up to Mulder's apartment. Struggles with herself on whether or not to egg him on with this new information.
Back at Doggett's house, Skinner shows up. Says he just got off the phone with Scully, "who was beside herself." Well, Scully apparently gave Doggett's information to Mulder. Mulder made it into the database and found a list of people who the government is tracking with certain genetic profiles. And now Mulder wants to "act on this information." Skinner is worried, because now he can't get a hold of either one of them. Doggett leaves to go find them.
Surprise, surprise - we find Scully waiting in a car in front of the Federal Statistics Center. Doggett raps on the car window and tells her to leave. Says he thinks someone set them up. She demands to know by whom. He says, "The same men who shoot first and ask questions later." Mulder is sneaking into the facility with the help of the Lone Gunmen (who are working Mission Impossible style). Doggett tries to follow Mulder in.
Mulder gets into the database room and onto a computer. Doggett bangs on the door and yells at Mulder to get out, that his life is in danger. Mulder ignores him. Doggett shoots the door open and tells Mulder he has to get out. Mulder accuses Doggett of being one of the conspirators. Says he is uploading the data on a list of people who have "been targeted because of their genetic profile for abduction and replacement by alien facsimiles." Doggett says that the information Mulder is copying will never make it out.
Meanwhile the calvary has arrived with humvees and big guns. Mulder accuses Doggett of setting him up. Doggett pretty much just throws up his hands at this point. Langly says that the information Mulder has tried to upload isn't working. Mulder and Doggett escape through the ceiling.
Doggett secretly meets with Rohrer again. And he is pissed. And he learns the lesson that Mulder has learned with all of his informants: Doggett needs Rohrer too much, despite knowing that he's being used, to turn him away. When Rohrer bends down to get water, the audience sees the bulge at the back of his neck. He's not human.