For the last part of this rather complicated story, starts with the tag line ‘AMOR FATI’. We see Mummy Mulder worrying about her son who’s still in hospital.
She leaves him to sleep when Smoking man pops in to say hi to Mulder. Smoking man doesn’t speak, but instead telepathically talks to Mulder, stating that he is Mulder’s father! This massive statement gets put on hold for a while, while Mulder is injected with something given to him. What we know now is that Mulder starts living in a dream world while smoking man kidnaps him and takes him to a DOD base.
Scully is working on her own investigation when she is visited by Kritschgau, with a small threat stating that since she has access to Mulder she needs to help. He goes on to explain that 2 and a half years ago, Mulder was infected with an alien virus (when he was in Russia with Krycek, season 4), and that now he’s been close to the alien power source, it’s reactivated.
Scully needs to help Mulder expose this. Since he is living proof of alien life. He goes on to say that if she destroys the virus killing him, he’ll destroy Scully. Next thing we know Mulder has gone from the hospital, supposedly removed by his mother – after checking CCTV, Scully see’s Mummy Mulder talking to smoking man.
Scully goes home to see Albert Hosteen standing in her living room (the Cherokee guy who nursed Mulder back to health), he informs Scully Mulder needs to be saved in order to save everyone. Meanwhile the rest of the episode is played out in Mulder’s head. Smoking man offers him a perfect life where he can leave everything behind.
He’s given a house just down the road from CGB Spender, Deep Throat pops in to say hello, and Diana moves in to sleep with him and raise some children. Back in the real world, Scully gets a book which details the mysteries of the world, and includes some of the characters she saw in Africa. It literately explains the sixth extinction, and the apocalypse.
She calls up Skinner asking where the book came from. He doesn’t know. As she heads of his office an unknown man is seen running away, and Skinner has been attacked – though not seriously. Scully can’t chase as he’s hit the fire alarm on the way out. She then heads to Kritschgau’s place and finds he has access to her files.
She deletes them ad Kritschgau explains it proves Mulder is biologically part alien. Mulder see’s his sister in the dream world, but we then flip to the real world which shows him on a operating table with Smoking man and Diana looking over him. Smoking man explains that Mulder is the key, a resistance against the alien virus. Scully finds Diana at FBI central (complete with cigarette smells!) and goes on to remind her just how Mulder was in the beginning, and that if she knows where he is, she should be doing all she can to help Mulder fight his battles, and bring the truth out.
Smoking man gets ready for an operation with Mulder, and states Mulder is immune to the apocalypse, and that Smoking man will carry the burden from now on. Scully see’s Albert again and they pray for Mulder. Smoking man lies next to Mulder on the table and the doctors begin an operation.
In his dream world, Mulder witnesses the end of the world, while Kritschgau is killed by Krycek!. Scully is seen in Mulder’s head being the only voice telling him to still fight – and she then finds him using the DOD card that was slipped under her door. One week later and Mulder and Scully have a rather emotional moment outside his apartment where Scully confesses she couldn’t find a cure for Mulder, or even find him in time before an operation was done on him. Mulder explains that Scully was the one friend, the one voice he listened to, and it saved him.
They hold each others faces and kiss lightly on the forehead. Mulder tells Scully that Diana was found dead, Scully realises it was her who gave her the book, and Albert has been in a coma for the last 2 weeks and died, there was no way he could have been at Scully’s place.