Regarding the shakeup at WANTF:
It appears that, Captain Wayne Robertson (the former head of WANTF) reassigned some agents, because he felt that those officers weren't effectively doing their jobs. The officers that Captain Robertson reassigned, then filed a complaint with Police Internal Affairs, based on some misconduct that has occurred under Captain Robertson's orders. I'm not sure if Captain Robertson no longer being the head of WANTF was a voluntary or involuntary move; however, it is clear that the investigation by Police Internal Affairs is what prompted Captain Robertson's reassignment.
Obviously, Captain Robertson learned the hard way, that if you're going to play loose with the rules (as WANTF often does), then you've got to take care of your subordinates.
Also, this is a picture-perfect example of poetic justice. Captain Robertson made a name for himself by using rats (narcs) to do his dirty work for him, and an investigation by Police Internal Affairs (sometimes known as the "Rat Squad") is the reason he's no longer the head of WANTF.