It was a rescue mission. You had gotten captured by the Foot Clan [more specifically Karai] after sacrificing yourself so the others could escape. And Raph was angry. Angry at the Foot, angry at Karai, and angry at you. But his anger came from a place of care and worry though

So Leo, Mikey, Donnie, and Raph sneaked into the Foot’s headquarters and found you bound and gagged in the middle of the room. Rushing over, Raphael knelt beside you as you tried to mumble out “it’s a trap”