I think what you're missing here is the implication.Not only is Flynn COOPERATING,but Mueller allowed him to plead guilty to a relatively minor charge.That means there are far worse charges they are going to excuse,and that means he has something of value that makes his cooperation relevant.A deal has to be beneficial to both parties involved,so it would make no sense for Flynn to plead guilty AND cooperate if the only issue he faced was lying to the FBI.
And why lie to the FBI in the first place,if it was all harmless?Remember Clinton was not impeached over Whitewater,even though that was the basis for the Starr investigation initially.The eventual charge was lying under oath,and it essentially involved a question regarding a sexual experience.
Trump will now downplay his relationship with Flynn.Yet the fact remains that for some reason he felt the need to intercede with Comey and attempt to limit the scope into the investigation into the actions of someone that he now claims he barely knew.There has to be a reason Trump got involved in the first place.
Could a possible scenario be that Flynn asked Trump for help and Trump in turn agreed to get involved which led to Comey's firing? Is it possible Flynn is willing to testify that he and Trump cooked up the plan,which essentially amounted to an Obstruction of Justice? There has to be a reason that Flynn is willing to plead AND cooperate,because it makes no sense to plead guilty to "lying" if that is the worst charge that you faced.
