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She uses a small spacecraft to escape the Pirate Ship and fires a missile to destroy it. As long as the Pirate Boss does not interrupt the battle, Samus will win.
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If Samus chooses to escape the Pirate Ship without successfully retrieving the Metroid capsule from the control room, she encounters the M=M in the docking bay. This results in a bad ending where she is unable to complete her mission and solve the mystery of the capsule. However, she forgets the Metroid capsule aboard the spaceship, and it is lost when the ship explodes. In the latter scenario, Samus must first successfully defeat the M=M with missiles and then successfully reach the escape pod in time. If the engines of Samus's spaceship go out of control, Samus can choose whether to escape immediately or finish off the Metroid=Mutant first. While not a video game, this game book features multiple endings resulting from the choices made by the reader in the final story arc. 27 August 2007 Metroid: Zebes Invasion Order