|Japan||Shogakukan||July 19, 2008||ISBN 4091406653|
|United States||VIZ Media||May 5, 2009||ISBN 1421527017|
|Singapore||Chuang Yi||September 7, 2010||ISBN 9789814306829|
- The Ruler of the Reverse World Appears!
- Target: Shaymin!
- Zero's True Ambitions Revealed!
- The Battle to Save the World!
Differences between the anime and the manga
| This section is incomplete.|
Please feel free to edit this section to add missing information and complete it.
- Zero's design is slightly different, as his right eye is often visible.
- The events of the story are clarified to be covering roughly six years. This is not mentioned in the anime version.
- The design of the Megarig is slightly different. The interior where Zero pilots the craft does not have his control chair right next to the video screens and keyboards, instead having a noticeable gap between them.
- Ash helps Newton destroy the Megarig from the inside by attacking its computers.
- Zero's final weapon is identified by name as "Mecha Giratina." It is not named in the film.
- Zero's fate is left unrevealed; he is last seen blacking out inside the cockpit of the crashed Mecha Giratina but is never shown getting out.
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