I'd like to think that one of two things occurs: Jane goes to jail, escapes, and the show takes on a "catch me if you can" type storyline with Jane using his smarts (much like RJ) to stay a few steps ahead. They set this up VERY well by having Abbot find out exactly where Jane was even with Jane being cautious and clever.

OR

Jane goes to jail, then the FBI agrees to his terms bc they are up against a mastermind criminal they cannot catch and think Jane is their only hope...and presto, another supervillian/adversary is born for Jane.

If he joins the FBI as is with Abbot's rules the show is WAY WAY too much like white collar, or House (when House was on parole) and they may as well cancel it.