In Aftermath 1, Scully and Mulder finally have it out over Diana. Mulder reveals the place she once had in his life (as lover, not wife) and his reaction to her departure years before. He tells Scully that even if they suspect her loyalties, Diana has access to the information they need and they must work with her. Indeed, they must trust her. Mulder and Scully reconcile their anger, but do not establish a clear path for their relationship.

In Aftermath 2, Mulder and Scully catch up with Diana and work out plans to capture Gibson and Cassandra (yes, she's still alive). Scully accompanies Diana to Arizona, albeit skeptically, and ends up the prisoner of CSM. Her implant is removed as a means of coercing her cooperation. Krycek releases her for his own ends. In the meantime, Mulder seeks Cassandra who is being held at an abandoned military base. He is led into a cyber-trap, but first stumbles across files related to the abductions and experiments. In his sister's folder, he finds a cache of photographs, including one in which a shadowy man in the background appears to be his father. In another shot of a group of girls, one of them looks remarkably like a young version of Diana Fowley. Finally, it is revealed that the vaccine/anti-serum is corrosive and gradually dissolves the body from inside. Sufferers leave a tell-tale sticky residue on things they touch. The key phrase from this story is "Trust is never enough to rule out betrayal."

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