The story begins as Grovyle, the playable main character, and Dusknoir lay on the ground unconscious back in the future. After waking up, Grovyle realizes the future is still dark, but reassures himself that the player and partner simply have not set the Time Gears in place yet. He is then spotted by a Sableye, who runs away. Dusknoir wakes up as well, but his injuries prevent him from attacking Grovyle. Grovyle then decides to travel to Temporal Tower and confront Primal Dialga, to buy his friends some time. He heads out into the Barren Valley with Dusknoir in pursuit.