It's pretty simple. NFL says "Patriots, you do bad?" Patriots say no, we will fully cooperate. NFL asks Patriots to do stuff. Patriots, thinking they did nothing wrong, do said stuff. Patriots ask the two jokers for their phones because the NFL wants them, then stop short of forcing Brady to turn his over once they realize he was in on it. So now the Pats have said they're going to cooperate fully, but once they realize the reality of the situation they can't or it will become abundantly clear Brady and these two jokers are behind it, so they stop cooperating while still pretending from a PR perspective that they are. That's why Kraft is acting like they did everything right and they allowed the NFL to speak to these guys 4 times, but in reality Ted Wells group only had one meeting with "the Deflator" before the pats put a stop to that shit(first three were just with NFL security before they got this evidence) and Brady immediately stopped cooperating after one initial meeting once it became clear he was going to be implicated. Basically the Pats know what happened now and they only forced their employees to cooperate up until the moment they realized there was actually foul play.
If the Pats were really as butthurt about this as Kraft is pretending to be they would force Brady to turn his shit over as his employer, show he had no illicit communications regarding doctoring the football, and tell the league to go to hell. But they can't do that, because he did know, and as soon as that became clear they immediately shut down contact with the guilty parties through the NFL.
