So they were like...classmates, and for whatever reason Jack decided he could actually tolerate John and they struck up a friendship. In the assumed usual Time Agent-y way it got physical. John took longer to graduate due to disciplinary issues, and they kept Jack around for teaching purposes, I guess, instead of sending him into the field right away.  Lara joins up, after a few years John graduates, gets partnered with Jack. On their first mission, they get sent out to intervene in something (a diplomatic mission, maybe?) which they botch due to John and his tendencies, which gets them stuck in a time loop for two weeks (felt like 5 years) where they’re basically kept as hostages. Sort of a "give me what I want and I'll let your guys go" deal.  <Ashley wrote the explanatory fic, will get added in at some point>

After that, John gets put on probation while Jack gets reassigned to a teaching post (with John as a TA as part of his probation), which he keeps full-time until John’s back on full duty, since in light of the mission it becomes crystal clear to the agency that Jack’s the only one that can keep John somewhat under control. During this time Jack gets the “most heroic” or whatever award (5099 AD, for reference). Once John’s probation is over, they go back to doing a lot of missions, and Jack teaches in his spare time.

At some point, Jack finds something funny, like a student suddenly drops off the face of the earth and everyone just dismisses it as "oh, they left". But Jack knows said student very well, and knows they wouldn't, so he starts this little side project and discovers that people tend to go missing (not entirely sure why, we'll get there…maybe they're using these people in some kind of super soldier program?). Anyway, it takes him about two years to uncover this and gather all the evidence and everything and he finally goes and confronts his superiors about it. They freak, but they know they can't just have Jack Harkness, of all people, suddenly disappear, it'd be too noticeable, so instead they wipe the whole thing from his memory.

After he figures that all out, he confronts the guys in charge about it. They don't take kindly to it and wipe his memory of the last two years, which probably confuses the fuck out of John. John brings the fact of the missing time to Jack's attention, Jack gets pissed off, and leaves. and I'm thinking it's a FAST progression from the meeting to Jack leaving. (around 5130 AD for reference, although probably tweakable)

So Jack's striking out on his own, doing his own thing, which leaves John at the Agency, Jack-less.   We'll assume he doesn't exactly take it well, what with the numerous rehabs and all, but he stays on since, seriously, what else is he really gonna do?  So he probably gets a new partner but goes rogue, since Jack's not there to keep him in line anymore, and gets even more reprimands/citations/probations than before. Somehow he still manages to be kept on because he's good at what he does, and he continues working for them until the Agency gets shut down. We'll assume it’s because the government or whatever finds out about their little project

*takes place near the end of the two years that Jack loses / present day*