Escape Again is the twentieth issue of the series and the second season finale.
Samus hooks her arm cannon up to the Phazon in the lair and uses the new Phazon Beam to destroy Metroid Prime. However, it reforms again, as Dark Samus. Samus tries to run forward but is yanked back because her cannon is still hooked up to the Phazon. She shoots another Phazon Beam at Dark Samus and destroys it. She gets in her ship, which has somehow been repaired, and flies away.
Dark Samus's arm cannon rises out of the ruins of the lair.
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Another New Beginning