The game starts with the player transforming from human to Pokémon with no memory.

After a bit, Grovyle starts stealing Time Gears at places, causing time flow to stop in those areas.

Dusknoir is a famous explorer joint effort with the Guild (that the player is in) to catch Grovyle.

Dusknoir says that he is from the future to catch Grovyle, who is also from the future. Dusknoir says that Grovyle wants to stop time flow because he is evil.

Then when Grovyle is caught, Dusknoir goes back to the future via a portal.

At the last moment, he grabbed the player and the partner into the portal.

Turns out that:

- In the future, time has stopped.
- Grovyle tries to change the past.
- Dusknoir doesn't want that to happen.

And in the later part of the game Grovyle is the new ally and Dusknoir is an enemy.

... and all this twist is in the context in which you will never see that coming