The guys can quit their jobs, move to Montana, and start farming sheep. They can lose the official badges and start their own detective agency. You can write WWIII and the aftermath, showing how their police skills serve them as a depopulated country tries to rebuild its infrastructure. Knock yourself out.

Just...don't go too far. I can't emphasize enough that this is fanfiction. Your readers are people who presumably like these characters. You can take the men out of the job, but don't take the personalities out of the men. Mulder is going to be paranoid, intelligent, and obsessive, even if he's running a detective agency in Boise, Idaho, and tracking down rustlers. Jim is going to be a Sentinel, possessed of heightened senses and equipped with Army Ranger training, even if he's running a fishing trawler in the North Seas. And even if they kicked Blair out of the university, he's still an anthropologist and a scholar. That's the way he approaches life and you have to keep that about him in order for your Blair to be the reader's Blair.

If you turn Blair into some fanny-shaking flamer, then he's not really Blair, is he? If you write Mulder as a hapless, inept detective, then that's not Mulder.

I've written this before, but it bears repeating. If you don't like Mulder's character on the X-Files, write your own darned OC. Don't distort, twist, and deform Mulder into someone you like. Keep one eye on canon as you write. Make sure, if you take the guys on a wild journey, they at least start somewhere recognizable.

In a further note, beware of reinterpreting history. Don't take the Mulder of a late-canon episode, under a moment of extreme tension, and go back and rewrite the earlier Mulder that way. Characters grow and change in a series. Mulder wouldn't have reacted, in the early days of the X-Files, the way he reacts to some events later.

What Blair and Jim are to each other in Sentinel Two is not what they were in the second episode of the story. Blair was still looking at a dissertation when he looked at Jim, and Jim still saw a necessary evil when he looked at Blair--someone he needed to teach him to control his senses as quickly as possible, and then get rid of.

The trust MacLeod has for Methos was not there the day they met. RayV did not start off by thinking Fraser was someone he wanted to know.

Revisionism is an ugly thing. Avoid it.