It's Almost Over, part 2 is the ninety-ninth issue of the series and part 2 of a 2-part issue.
The Future Writer asks Samus, Oveur, and the Writer what they think of his new powers. He admits that he is not capable of detroying the world. He then vanishes again. Samus approaches Oveur, the Writer, Mother Brain, Ridley, Kraid, Dracog, Pickett, and Bad Grammar Boy and tells them that they need to work together and trust each other (Oveur and the Writer shake hands during this scene). She then says that the final battle is beginning, and the last regular issue ends.
It's Almost Over, part 1
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