Near the end of the Hidden Land you come across the Rainbow Stoneship, where Dusknoir appears to take you back to the future. However, you, your partner, and Grovyle fight to avoid being captured. After winning, Dusknoir goes to attack you again but Grovyle blocks the way and gets struck. Grovyle then pushes himself into the portal with Dusknoir, leaving you and your partner behind. Grovyle's final words were "though the parting hurts. the rest is in your hands." You then take the rainbow stoneship and travel to Temporal Tower to save the world!
You can later replay this dungeon, however instead of with you, your partner, and Grovyle, now you can only go with you and your partner. However, the player still can not recruit Pokémon.