The battle to stop Team Galactic from creating a new world order rages on as our heroes, as well as Cynthia, Looker, and Team Rocket, mount assaults from different vantage points. All of Team Galactic’s evil plans seem to be progressing on schedule. When Cyrus calls forth the Legendary Pokémon Dialga and Palkia, it appears that a brand-new universe is about to be created right on Mt. Coronet, destroying the old world and everyone in it! But the three lake guardians Azelf, Uxie, and Mesprit have connected their hearts with Ash, Brock, and Dawn. After our heroes save the three lake Pokémon from Cyrus’s grip, their valiant and powerful group effort breaks the chains that have been holding Dialga and Palkia! The Pokémon are sent back to where they belong, which stops the excessive energy levels that threatened to destroy the entire Sinnoh region.
After Cyrus enters the vortex of his newly created universe alone, Team Galactic is finally defeated. Team Rocket slips away unnoticed, feeling vindicated and happily victorious with their defeat of the "fashion freaks." And Cynthia marvels at the way Azelf, Uxie, and Mesprit joined forces with our heroes, knowing for sure it’s all because of their great love of Pokémon!
After being Teleported into Team Galactic HQ, Ash and his friends rush to rescue the subdued lake guardians. Mars's Purugly and Jupiter's Skuntank slam them back with Iron Tail attacks. Pikachu, Piplup, and Croagunk are distracted, exposing them to Toxicroak's Sludge Bomb attack, knocking them down. They notice the Red Chain fragments on the lake guardian's foreheads, which Cyrus and Charon fill them in. As a result of the fragments, the three Pokémon are now under the control of the powers of the Original One. Intending to fulfill his quest of creating a new world, Cyrus walks out with the lake guardians, leaving Ash and his friends trapped by Team Galactic.
Team Galactic leaves their headquarters for Spear Pillar via helicopter with Ash and his friends imprisoned in the same helicopter. Cynthia spots the chopper from the ground and follows in her SUV. Looker and Team Rocket, having neutralized the Team Galactic Grunts stationed at the entrance to Spear Pillar, pretend to stand guard with the intent of ambushing Team Galactic. As Team Galactic arrives and exits the helicopter, Looker silently recognizes Cyrus while Team Rocket recalls his manic speech in the Celestic Ruins. However, Cyrus and his Commanders easily see through the disguises which results in them being incapacitated by a Flamethrower attack from Jupiter's Skuntank and being put in the helicopter's cell with Ash and his friends.
Outside the gate, Saturn uses the Spear Key to unlock the gate to the Spear Pillar, the key being absorbed into the gate and changing form. Cyrus opens the gate with his Red Chain-embedded glove, opening the pathway. The path lights up, leading down to the Spear Pillar as Cyrus and his supports head inside, except for Jupiter. Moments later, as Jupiter grows bored of having to wait, Skuntank is suddenly struck and knocked out by a Giga Impact from Cynthia's Garchomp. Cynthia confronts her as Garchomp restrains Jupiter before she can call out another Pokémon. Cynthia then frees Ash and his friends and imprisons Jupiter and the Team Galactic Grunts. Though Jupiter insists it is too late, Ash and his friends proceed into the Spear Pillar to stop Cyrus.
Inside the Spear Pillar, Cyrus and the others reach their destination, placing the Adamant and Lustrous Orbs, as well as the lake guardians, in position around the ancient altar. Cyrus uses the power of the Red Chain to force the lake guardians to use their energies to power the Orbs and begin to summon Dialga and Palkia. Charon then gives the order to fire, and two bolts of Red Chain energy are shot from a cannon around the formations of two dimensional energy portals. As the portals begin to take shape, their powers begin causing atmospheric disturbances around Mount Coronet, which Professor Rowan and Gary pick up from their Sandgem Town lab. Dialga and Palkia start to appear at the Spear Pillar, and the Red Chains wrap around both. Pikachu, Piplup, and Croagunk fly in on Staraptor, Garchomp, and Gliscor, destroying the cannon. Saturn sends out Toxicroak, but Croagunk leaps down from Gliscor and knocks his ultimate foe out with a Brick Break to the head before it can even act.
Though Cynthia is awed to meet the lake guardians, she states that never wanted to see them this way. Mars sends out Purugly and the Grunts send out Golbat, but Pikachu and Piplup easily defeat them, allowing Ash and his friends to proceed. Pikachu, Piplup, and Croagunk free the lake guardians, destroying the Red Chain fragments on their foreheads. Ash recalls Staraptor and Gliscor into their Poké Balls and he, Dawn, and Brock retrieve the lake guardians. Dialga and Palkia start to fade, and Cynthia states that Cyrus has lost; however, Cyrus has a backup plan. He summons more power from the Red Chain, and the formations begin to glow, causing Dialga and Palkia to finally emerge in full form. The Pokémon strain under the power of the Red Chain as it takes control of them.
The lake guardians tap into their powers as they telepathically ask Ash and his friends to free Dialga and Palkia. Cyrus orders the Legendary Pokémon to use their powers, creating a portal into another dimension that will expand outward and consume the old world, causing the effects of the disturbances around Mount Coronet to intensify. Ash and his friends try to attack the Red Chains holding Dialga and Palkia, but Cyrus has the Legendary Pokémon use their signature moves, Roar of Time and Spacial Rend, to stop Pikachu, Piplup, Croagunk, and Garchomp's attacks. Dialga's Roar of Time also proceeds to strike Ash and his friends, but the lake guardians block the attack with Protect. Saturn and Mars want to go into the new world with Cyrus, but he turns on them, revealing his true intention of having the new world to himself. Ash and his friends attack again, this time with the aid of the lake trio's Extrasensory attacks, destroying the Red Chains and freeing Dialga and Palkia. The portal begins to shrink, but Cyrus walks up and gets drawn into it before it fades. Mars panics and wants to go too, but Saturn holds her back as the portal begins to fade away.
However, Dialga and Palkia continue to rampage, using their signature attacks on the fading portal, creating a massive black hole of negative energy that threatens to envelop and destroy the Sinnoh region. Cynthia warns them of the impending danger as the lake guardians plead with Ash and his friends to do what they can. Ash and Azelf destroy the black hole with the latter's Explosion attack. Next are Brock and Uxie, who telepathically communicate with Dialga and Palkia to calm their rage. Lastly, Dawn and Mesprit heal Dialga and Palkia, much to their happiness. The lake guardians create a portal that sends Dialga and Palkia back to their isolated dimensions, reversing the energy levels and clearing the area around Mt. Coronet.
The lake guardians celebrate with Ash and his friends. Ash asks them why he, Brock, and Dawn of all people were chosen to synchronize with the Pokémon. Cynthia believes that the trio sensed the strong love that Ash and his friends have for all Pokémon. The lake guardians then depart, leaving Ash and his friends to wonder when the day will come that they meet again. Later, Professor Rowan and Gary arrive. The Adamant and Lustrous Orbs are secured as Gary decides to take them back to Professor Carolina in Celestic Town. Team Rocket makes their getaway, rejoicing that now that Team Galactic is gone and the world safe, Team Rocket can continue their plans to rule the world. The police take Saturn, Jupiter, and Mars into custody, officially dismantling Team Galactic. Cynthia thanks Ash and his friends for saving Sinnoh as they continue on their journey.