In the throne room, Fawful and "Bowser" talk about how easily the minions were duped. It is then revealed that "Bowser" is actually Bowletta, who has shapeshifted into a fake Bowser. A Lakitu, who was hiding, overhears their conversation and reports to the four captains.
However, it is revealed that they too were already aware that the Bowser they encountered was a fake, with Captain Goomba remarking of when he told him to "destroy" Mario and Luigi, and how the real Bowser would not go to those lengths. When the brothers arrive at the castle, the captains instead decide to confront Fawful and Cackletta.
As the four captains force the dastardly duo to surrender, Fawful opens a trapdoor to send them beneath the castle. They end up finding Fawful-like robots. Realizing that this is their final battle, the four captains know that the Mario Bros. will defeat Bowletta. The Goomba Sqaud will fight Mechafawfuls (X, Y and Z), Lakipeas, Gritty Goombas, Paratroopeas, Clumphs and X, Y and Z variations of Fawful. With Fawful ultimately defeated, Prince Peasley informs the captains of Bowser's whereabouts. They exit the room whilst flying on Captain Boo.
After defeating Cackletta, Bowser wakes up, remarking on how he was going to kidnap Princess Peach, when he meets the four captains. After happily reuniting with their king, they then noticing the castle violently shaking as it begins to explode. As the captains end up in Beanbean Fields, they find Bowser in a present box, being carried by a plane that the Mario Bros., Peach and Toadsworth are riding back to the Mushroom Kingdom, in which they chase the player home.
At Bowser's Castle, Captain Goomba is summoned by Bowser as he promotes him to lead the Koopa Troop as they watch on. Then, Bowser gains a feeling that they have met before, and a flashback plays to when Captain Goomba lands on Bowser at Hoohoo Mountain, causing him to get amnesia, which led to him becoming Popple's sidekick and possessed by Cackletta's spirit. Realizing the events caused, Bowser chases Captain Goomba, and is eventually demoted of his rank. However, the Koopa Troop never forgets about the bravery led by the Goomba.
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The 1st battle contains 4 Mechafawful Xs, and 4 Lakipea. The enemy captain is a Mechafawful X, and it knows Chance and Call for Backup. Call for Backup calls for a Lakitu.
The 3rd battle contains 5 Mechafawful Ys, and 3 Beanerang Bros. The enemy captain is a Mechafawful Y, and it knows Chance and Deny.
The 4th battle contains 3 Paratroopeas, 4 Mechafawful Ys, and 1 Most Furious Fawful Y. The enemy captain is the Most Furious Fawful Y, and it knows Call for Backup. Call for Backup calls for a Mechafawful Y, Mechafawful X, or Mechafawful Z.
The 5th battle contains 4 Clumphs, and 4 Mechafawful Zs. The enemy captain is a Mechafawful Z, and it knows Rally and Deny.
The final battle contains 1 Mechafawful X, 1 Mechfawful Y, 5 Mechafawful Zs, and 1 Most Furious Fawful Z. The enemy captain is the Most Furious Fawful Y, and it know Rally and Lightning.
After the final battle, Bowser Jr. (Lv. 35) is recruited.
• ⋆-Enemy, boss, or stat exclusive to the main game. • ⋆⋆-Enemy, boss, or stat exclusive to Minion Quest: The Search for Bowser. • ⋆⋆⋆-Enemy variants differ in Mario & Luigi: Superstar Saga + Bowser's Minions.
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