Iron man clashed into Thor and they began to fight including America. Once it was over, Loki and Harley were transported to S.H.I.E.L.D to be locked up. They were locked in seperate cages in order for Harley to be in space  away from him. 

"....you talk about peace, warp an innoccent girl's mind, and you kill cause its fun. You have made me very desperate" Fury finished his chat with Loki before he left the room.