In The Rise of Darkrai, Dialga engaged in a massive battle with its enemy, Palkia, wounding it and causing it to flee to Alamos Town, hiding itself and the town in another dimension in order to protect itself. However, Dialga reappeared when Palkia's cover was blown by Darkrai, aggressively attacking the Spatial Pokémon and resuming their battle. Eventually, Palkia began charging its Spacial Rend and dared Dialga to give it its best shot. Dialga rose to the challenge and powered up its Roar of Time. Before the two combatants could finish each other off, however, Ash and Dawn magnified the volume of the song "Oración", which calmed the Temporal Pokémon. Dialga and Palkia stopped fighting, and Dialga looked at Ash and Dawn as it flew away.
In Giratina and the Sky Warrior, black, poisonous clouds had overlaid the once beautiful and law-breaking Reverse World. The cause of this was Dialga's and Palkia's prior battle, which angered Giratina. To get revenge, in a lake, it dragged Dialga into its own world. There, Giratina and Dialga did battle. Every moment, Dialga tried to escape; however, Giratina continued to pull it back into the Reverse World. Finally, thanks to Shaymin, Dialga was able to run away, but not before enveloping Giratina in a time loop to trap the Renegade Pokémon in the Reverse World in order to fully escape. Dialga made a small appearance at the end of the movie, in which Giratina went to attack it again.
In Arceus and the Jewel of Life, it was revealed that the reason why Dialga and Palkia clashed in Alamos Town was because their dimensions, which are not meant to ever intersect, intersected due to Arceus preparing to awaken. As a result, Dialga believed that Palkia had invaded its territory, a mistake shared by Palkia. Sheena used her ability to summon Dialga to save Pikachu and Piplup and when Giratina showed up to attack Sheena used her powers to touch a Pokémon's heart to end the battle once and for all. Later, when Arceus arrived and prepared to eradicate humanity for its previous betrayal, Dialga, along with Palkia and Giratina, protects Ash and friends from Arceus's attacks, and uses its temporal abilities to send Ash, Dawn, Brock, and Sheena back in time to give them a chance to change the past to save the future. Dialga was then badly injured by the Alpha Pokémon alongside Palkia and Giratina, and exhausted due to time travel. Eventually, when Ash and the others had successfully changed the timeline for the better, Arceus healed Dialga and the others and Dialga returned to its own dimension to live peacefully once again.
