IIRC, Cohen fell into Mueller's investigation through other means than being a target like Manafort, they weren't particularly interested in him too much, the Sovereign District was going after him and when they raided his office they just shared the results with other investigations. Cohen's been running all over for the last 18 months, fighting with Justice/FBI, and it was only the last couple that the Mueller investigation took any interest in him because of stuff found in his seized records.
His guilty plea is mostly about tax evasion and misreporting on financial reporting/donations, he doesn't have a plea to cooperate or anything unlike Flynn who is never going to be sentenced apparently. Cohen's going to get five years or something I think I read.
I have no proof obviously but I think Mueller probably wants to steer well clear of the Stormy Daniels, etc. type stuff. He could have folded all that into his investigation like Ken Starr did.
