Jafar will request Mickey's assistance in locating him with the quest, Cry Fowl. After the quest has been activated. Iago will appear in the Cave of Wonders: Inner Reaches, where he will initially be uninterested in returning... Until Mickey mentions that the evil witch could come by at any minute. At this point, Iago is only too happy to return to the Fortress.
Once there, he will remain in Jafar's Room.