Bulbasaur, a pokémon that wants to join a rescue team, finds a pokémon named Torchic on the beach. Torchic explains how he lost his memory but remembers that he was a human.
Torchic and Bulbasaur create a rescue team and, saving pokémon and discovering new secrets, become great friends.
But one day, someone starts stealing something called "Time Gears", stopping the flow of time in that area.
Scared and shocked, Torchic and Bulbasaur set out to stop him. Along the way, they find out that his name is Grovyle and that he is trying to save time by bringing the Time Gears to Dialga. They also find out that he's from the future where there is no time and that his partner is Torchic, but they got separated on the way to the past.
Torchic and Bulbasaur help Grovyle bring the Time Gears, but along the way, Torchic finds out that if he and Grovyle succeed, the future will change, and they'll disappear. Grovyle brings their enemy Dusknoir back to the future so e can't interfere. Torchic continues anyway and together, he and Bulbasaur succeed.
Not long after, Torchic disappears, and Bulbasaur returns to Treasure Town where he tells the story so that Torchic will live on in the hearts of the pokémon.
Dialga watches Bulbasaur from his tower, and decides one day that, to pay Bulbasaur back, he would bend time and bring Torchic back.
Meanwhile, in the future, Dusknoir and Grovyle team up when they find out that Primal Dialga has a new henchman.
But Dusknoir turns on Grovyle. He traps him in between crystals that will melt his soul. Dusknoir then explains his plan.
He will melt Grovyle's soul then use his body to go back to the past. Torchic and Bulbasaur would welcome him as their friend and then he would attack them.
Grovyle talks to Dusknoir until finally Dusknoir has a change of heart and saves him. Then, Grovyle, Dusknoir, and Celebi travel to stop Dialga.
They beat Dialga, and time slowly starts to resume. But with the time going again, Grovyle and the gang know their time is up.
Dusknoir disappears, knowing that his spirit now shines.
Grovyle holds Celebi as she watches the world slowly come into motion.
When they all disappear, a mythical happens. A powerful being brings them back. And Primal Dialga becomes Dialga again and the future is once again in peace...
