A few weeks post the events of the film, Mulder appears before an FBI panel to review justifying expenditure, travelling to Antarctica and the future of the X Files. Assitant Director Skinner tells Mulder in an awkward conversation, that the request for The X Files project to be re-opened has been denied, however he's left a case file pertaining to the X-Files on his former desk. Mulder then goes to his old office to find that the project has been taken over by Jeffrey Spender (Chris Owens) and Diana Fowley (Mimi Rogers). Angry, he leaves the office and with the help of his partner Scully, starts an investigation into an escaped alien - the file Skinner had left Mulder - going against orders from their new superior, Assistant Director Alvin Kersh (James Pickens, Jr.)
Mulder and Scully eventually learn that the cigarette smoking man abducted Gibson Praise (Jeff Gulka) - during the season five finale 'The End' - in the hopes that he can communicate with and find the alien, as he himself is biologically part alien. Scully discovers that Praise has the alien virus in his blood, when she brings him into the hospital to do more tests on him again.
Later, Alex Krycek (Nicholas Lea) - a former rogue FBI agent and assasin for the Syndicate group - poisons Skinner with a nanorobot infection. He periodically continues to control the nanotechnology within Skinner's system, to achieve his goals. In short, if Skinner doesn't do what Krycek wants, his life in over at the push of a button.
A few months later, Mulder and Scully discover reports of rebel faceless aliens, setting ablaze doctors who were working on Cassandra Spender (Veronica Cartwright,) - ex wife of the cigarette smoking man, mother of Jeffrey Spender and an alien abductee. Skinner and Spender head to where Cassandra has been found and asks for Mulder, where Jeffrey reluctantly agrees in spite of the fact he feels Mulders alien conspiracy theory in nonsense. Cassandra tells Mulder and Scully that the aliens are coming to wipe out the human race. She claims that the rebel faceless aliens are mutilating their faces, in order to prevent being infected by the black oil. Fowley agrees to help the cigarette smoking man - after he reveals everything to her - to betray Mulder despite still having feelings for him.
Later on, Cassandra escapes the hospital arriving at Mulders apartment, insisting that he kills her because she doesn't want the project of the Syndicate to continue - as she has been an abductee for over 25 years and is a success story for the Syndicate - because if the aliens learn of her existence, they will colonise the human race.
Fowley arrives at Mulder's apartment with the Centers for Disease Control in order to abduct Cassandra. She says that a biohazardous contagen has been contracted by Cassandra which is a smoke screen to capture her and because of this, she says that because the agents have been in contact with her, they need to be quaranteened. While there, Mulder notices Covarrubiaswho informs Mulder that she'd been a subject of the Syndicate experiments, although they were different to what Cassandra experienced, as they were testing a vaccine on her against the black oil, whereas with Cassandra, they were creating an alien-human hybrid.
Elsewhere, the Syndicate are waiting in an air hanger with their families and children in the hopes of meeting the alien colonists, however they're met by the alien rebels who set everyone ablaze, including Cassandra, although the cigarette smoking man and Fowley escape. Spender is later shot in the X-Files office by his father and later assumed dead.
Several months later, a metallic artifact is discovered on a beach on the Ivory Coast in Western Africa. The artifact has inscriptions on it and starts affecting Mulder by giving him severe headaches and he starts hearing hundreds of voices all at once. He later develops telepathic abilities and can read peoples thoughts. Mulders old colleague and friend Charles Burks, a.k.a. Chuck (Bill Dow), says that after taking a look at the inscriptions, the symbols appear to be Navajo. Soon thereafter, Mulders state of mind becomes agressively aggravated and delusional and is placed under 24 hour observation in hospital. Scully travels to Africa in the hopes of finding an answer and a cure for Mulder and finds a large space craft buried on the beach, with the same inscriptions of the rubbing (metalic artifact.)
'Biogenesis,' the season six finale, is by far my favourite episode of season six, as it's part one of a three part episode continuing into season seven. It also shows things happening to Mulder, as everything usually happens to Scully, so this is a good change.
I hope you've enjoyed this overview, stay tuned for the season seven overview coming up in about two weeks.