Methos (or other character who's not quite human/has special abilities) is captured by the NID, who do Bad Things to him because they know about his abilities.  The SGC mounts a rescue, saves him, and asks him to join them because his abilities would be useful.  But he's all "not just no, but hell no" because they might have rescued him, but they're part of the same thing.  Of course, they let him go because they're the good guys, and he disappears completely.  SG-1 keeps getting called in to investigate/to be accused of the destruction of NID bases.  There's a growing suspicion that Methos (or, well, whatever identity of his that they know of) is responsible; they find him destroying the last base.