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Arriving at the [[Hidden Land]], Lapras tells them that in order to reach the Temporal Tower, they must take the Rainbow Stoneship, located inside an old ruin. Finding the ruin, the partner is astounded at what they can find—pictures of legendary Pokémon {{p|Mew}}, {{p|Kyogre}}, {{p|Groudon}}, {{p|Dialga}}, and {{p|Palkia}} engraved on the wall. Proceeding further, they find a temple where, at the top, they find the Ruin Fragment pattern. The team discovers that the temple itself is the Rainbow Stoneship, and in order for the ship to operate, the Relic Fragment must be slotted in one of the indentations. But before the partner can do so, they are captured by Dusknoir and the Sableye entourage. Dusknoir takes their captives to a nearby Dimensional Hole, but before the team can be put through it, they overwhelm the Sableye, prompting Dusknoir to fight back. The team is able to defeat Dusknoir in battle, but while the partner goes to activate the Rainbow Stoneship, Dusknoir warns that should they succeed in their quest, the Pokémon of the future, including the player and Grovyle, will be erased from existence, because they are from a future that will no longer exist. Grovyle admits that this is the case, but that their sacrifice is worth the trouble if it means that the future can be saved. The player accepts this fate, even though the player knows that the partner will not take it as easily as the player or Grovyle.
Meanwhile, the partner succeeds in activating the Rainbow Stoneship, but Dusknoir manages to recover and attack the player before either the player or Grovyle is on board. Just as Dusknoir tries to finish off the player, Grovyle intervenes. In a move of desperation, Grovyle pushes Dusknoir towards the Dimensional Hole, hoping that in his own sacrifice, Grovyle will erase Dusknoir from existence. Dropping the Time Gears, Grovyle pushes Dusknoir and himself through the Dimensional Hole, but not without giving his last goodbye. The partner recovers the Time Gears, and the team proceed on the Rainbow Stoneship, with the player keeping silent to the partner about his/hertheir fate. With a heavy heart, the team head towards Temporal Tower to take on their final mission.
Arriving at the top of Temporal Tower as the tower itself is collapsing, they find a mystical relic with five indentations. Before the partner slots in the Time Gears into the indentations, the team is attacked by none other than Primal Dialga, having just gone berserk. Realizing that there is no reasoning with Primal Dialga, the team prepare to battle it out to the end. After a long battle, Primal Dialga is defeated, and the partner takes the opportunity to install the Time Gears. The earthquakes destroying the tower eventually stop, and Dialga is restored back to normal. Dialga quickly uses its powers to restore the world back to normal, though Temporal Tower remains heavily damaged. Dialga explains that the world's paralysis has been prevented with the installation of the Time Gears, and that peace has been restored. Dialga says its thanks to the team, but also warns that the world can only be back to normal in time. Dialga shows the team out of the Temporal Tower, where the Rainbow Stoneship and Lapras are awaiting them for their ride home.
On the way back, the player feels the effects of being slowly erased from existence. The partner notices this, and wonders what is wrong. The player says his/hertheir goodbyes, regretting that the partner was kept in the dark on the player's situation. The player slowly fades out of existence as the partner makes their tearful goodbye. The partner returns home, crying, but knowing that the player has made the partner stronger. Back home, the partner tells the townsfolk and the guild everything—how they had traveled across the [[Hidden Land]], how Grovyle and the player had sacrificed themselves, and how they had saved the world.
Months have passed since the incident. The damages from time have slowly been healed, and life has returned to normal for most... but not for the partner, still mourning over the player's disappearance. At the beach, the partner is taking a walk, when the partner is reminded of the player and their adventures together, and how now the player is gone—erased from existence. The partner collapses on the beach out of extreme sadness, and starts crying. The end credits roll at this point.

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