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Captain Boo is one of the main protagonists of the Minion Quest: The Search for Bowser story mode from Mario & Luigi: Superstar Saga + Bowser's Minions.
He first encounters Captain Goomba and Captain Shy Guy in Chucklehuck Woods when he is busy working for a brainwashed Iggy Koopa in conquering Chucklehuck Woods, and he tries to toy with them, but they catch his act and reveal him. The two captains ask him to come with them and try to recruit him, but he says he's too busy helping Iggy. They then proceed to give him the full rundown on what happened to Iggy, but he doesn't understand any part of what they're saying. He complains that he wants to go home, and that he feels really upset, but that he doesn't want to disobey Iggy. Captain Shy Guy responds by saying what he's doing is disobeying Bowser, and with this, the Boo joins the squad and fights alongside Captain Goomba and Captain Shy Guy as they fight to rescue and reunite with Bowser. The two Captains make him a Captain as well after he asks for a flag to keep the sunlight from affecting him, which he is uneasy about at first. At the Cutie Battle Contest, he teases Captain Shy Guy only to get pelted by a Turnip from him. He also expresses his concern about Captain Koopa Troopa's rhyming at Teehee Valley before the latter joins as a Captain.
Captain Boo appears in Mario & Luigi: Bowser's Inside Story + Bowser Jr.'s Journey, where he is an enemy in the Bowser Jr.'s Journey mode. He fights alongside Captain Goomba, Captain Shy Guy, Captain Koopa Troopa, and King Bob-omb.
Captain Boo is often shown to be easily upset. He also has a teasing side, as shown in the "Cutie Battle Contest".