
Once you beat Dialga you go through a cut screen. During this Dusknoir attacks and tries to send you back to the future, but Grovyle sacrifices himself and send himself and Dusknoir into the future. With the help of a relic, that your partner had found and cherished since before you arrived, you are guided to Temporal Tower where you will battle the somewhat brainwashed Dialga to save the world from the distortion of time forever. Wigglytuff, the guild master take you to Lapras, one of his great friends. Afterwards you try to discover how the now collapsing Temporal Tower, home of the controller of time: Dialga. When you return, even though you are reluctant you take Grovyle to the guild where he is accepted as a friend. So you guys eventually escape and you break out of the future with the help of Celebi. Now you find out from Grovyle as you are being tortured that you were once his human partner and something happened as you tried to travel back in time that turned you into a pokémon. During this Dusknoir reveals that he and Grovyle are from the future then right as Dusknoir is about to take Grovyle through a portal to the future Dusknoir attacks and drags you along with him. Once the battle is over you are taken back to the town where their is a cut scene. Once Grovyle tries to take Azelf's time gear you, your partner and Dusknoir (the new ally) battle and capture him. You will also gain an ally pokémon who says he has been chasing after Grovyle.
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You will cross paths with bosses like Groudon, Mespirit, Uxie, and Azelf.

As the game progresses you try and stop Grovyle from taking all of the time gears which, once taken, freeze time in that area. After a while you will find out that a pokémon named Grovyle. You will then take on several mission making a small sub-story that will cross with the main story. You then go to the guild and get let in to apply as apprentices to the guild. He will tell you who he is and what his dream is (becoming an explorer).

Whatever partner pokémon you then choose will find you and will.

You start out, like the first game, as a pokémon without a name (which you pick at that point) and a memory. The storyline plays out throughout the game and technically never ends.
