Minion Quest: The Search for Bowser
Captain Boo first appeared in Minion Quest: The Search for Bowser as a ordinary Boo. He is first encountered by Captain Goomba and Captain Shy Guy in Chucklehuck Woods whilst working for a brainwashed Iggy. The two captains try to recruit him, but he tells him that he is busy working for Iggy. Then they try explaining to him what actually happened to Iggy, but he doesn't understand any of this. Boo then tells them that he wants to go home, but he doesn't want to disobey Iggy. Captain Shy Guy then tells him that he is actually disobeying Bowser. Realising this, the Boo joins the two captains and becomes Captain Boo.
Bowser Jr.'s Journey
Captain Boo returns in Bowser Jr.'s Journey as a enemy and a recruitable ally. Just like Minion Quest, he is a Flying-type enemy/ally.