Peter drops out of school and doesn't tell his mother. He spends all day at the library instead.
When the aliens take Scully and it's Mulder all alone in his office with nothing to do but wonder when it had become their office, Olivia is turning into a workaholic. There's a boy in her chemistry class who wants to ask her out, but she doesn't even notice - she's too focused on what she wants to notice what she can have. Eventually the boy gives up and sleeps with her roommate, but at least Olivia got an A on her chemistry final.
Peter leaves for good. His mother never sees him again.
When Scully gets cancer and Mulder's kneeling by her bedside stuck somewhere between weeping and prayer, Olivia graduates college and is considering her job options. She sits down with a Marine recruiter and thinks that maybe this could be the chance for what she's always wanted.
Peter is putting out fires in California and having the time of his life. His mother has a picture of him in one hand and an empty bottle of sleeping pills in the other.
When Mulder's brain goes funny and he has a weird dream where he's married to Diana Fowley and Scully is his touchstone, Olivia investigates a statutory rape case. She gets the evidence that puts the guy away, and her superiors tell her she did a good job. Broyles doesn't like her very much.
Peter goes a bit crazy and now he owes a lot of money to a guy who had his name legally changed to Big Eddie.
When Scully is pregnant and Mulder is missing, Olivia becomes an FBI agent. Olivia holds the door open for her once on the way to the parking lot and when she's gone Charlie tells her about Mr. and Mrs. Spooky. Olivia laughs. There's no such thing as aliens.
Peter falls in love, and it's a mistake from the very beginning.
When Mulder is arrested and Scully and Skinner and Doggett and Kersh are breaking him out, Olivia meets John, and the way he smiles makes her feel funny. But it's nothing, it'll pass in time, and she ignores it like she ignores everything else. But John doesn't, and Charlie notices but he doesn't say anything.
Big Eddie catches up with Peter. After he gets out of the hospital he decides it's time to get out of the country.
When Olivia is trying to save John's life and Peter is really very annoyed to be back in the United States, Mulder and Scully are making a new life in Ireland. Scully picks up a bit of an accent and Mulder teases her for it, but really he thinks it's cute and maybe, just maybe, they'll be able to build a life for themselves.
Skinner is able to keep his job, but he worries. He pins Mulder's poster up in his study at home and starts watching the sky and the newspapers.