Foot Clan
Raphael attempted to reconcile Michelangelo with his family in the Chasing Phantoms arc, in which he argued that Michelangelo should be with them, even if their new place was as part of the Foot Clan. However, he became increasingly uncomfortable with Splinter's methods. And upon Splinter's execution of Darius Dun, Raphael changed his mind and decided that Michelangelo had been right all along, leaving the Foot Clan along with Donatello and Leonardo, and moving back into their old lair.