When playing through the best game in the world, Pokémon Mystery Dungeon: Explorers of Sky, I realized that I had found a hole in the plot.
In the main storyline:
At the end of the main story, before the credits roll, you and your partner do battle with Primal Dialga and defeat him, then use the Time Gears to restore Dialga and time itself to its natural state. However your player, being from the future, starts to disappear as the future begins to right itself again. You finally disappear and your partner is devastated. However Dialga, now that his mind is stable, realizes how much the world owes you and brings you back.
In the Special Episode In the Future of Darkness:
While you and your partner are fighting Dialga in the past, in the future Grovyle, Dusknoir and Celebi are duelling with an even for ferocious Primal Dialga. They defeat him before he can damage the time stream, allowing you to put the Time Gears in place and save the world. The future begins to change, and the frozen planet begins to move. While your character is feeling the effects of time and begins to disappear, at the same time Grovyle, Dusknoir, Celebi, the Sableye, and the rest of the future Pokémon are also disappearing. First goes Dialga, then Dusknoir, then Celebi. It is only Grovyle left, and then he, as well, vanishes.
But soon after Grovyle disappears, everyone returns. Dusknoir, Celebi, Grovyle, Dialga, the Snorunt, Spiritomb… they're all living. Grovyle tells Dialga (who is now back to normal) that he is eternally grateful to him for saving their lives. Dialga then tells him that it was not his doing that saved them, for he is not powerful enough. He then reveals that it was the work of a "higher being". That being is Arceus.
Now, my question is this: How can Dialga have the power to save Pokémon from disappearing, yet not have that power at the same time?
In the story Dialga brings back the main character.
In In the Future of Darkness, Dialga says that he does not have the power to save Pokémon from disappearing.
This is a major contradiction. Is it simply that Dialga cannot save multiple Pokémon? Is it really Arceus' doing that saves you in the main storyline? I need to know!