So what happened with Karai and the Foot between seasons 5 and 6?

[neatoman]

So at the end of season 5 Karai was still leading the Foot (maybe ending the feud with the turtles, it's not very clear). At the start of season 7 Khan (a previosly unmentioned character) leads the Foot which are still enemies of the turtles and Karai just makes a silent appearence in the final episode. In Turtles Forever however, Karai locates the Shredder in the Technodrome and they promptly take control over the Foot again.

So what happened? Was Karai overthrown? Is the season 7 Foot a splinter group? Did they do their evil operations under her nose?
You could just say "Season 7 was the worst season, it's because of bad writing", which it is but that's not a very good answer anyway.

Edit: Crap! I meant to title this thread "So what happened with Karai and the Foot between seasons 5 and 7?".