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!
Directly from the last episode, Ash's Pikachu and Dawn's Piplup use their attacks to breach the tanks holding the lake guardians. As Ash and his friends rush to rescue them, Mars's Purugly and Jupiter's Skuntank push them back with Iron Tail attacks. Pikachu, Piplup, and Croagunk are distracted, exposing them to Toxicroak's Sludge Bomb attack, putting them down. They then notice the Red Chain fragments on the lake guardian's foreheads, which Cyrus and Charon fill them in, the Pokémon now under the control of the powers of the Original One. Intending to fulfill his quest of creating a new world, he walks out with the lake guardians, leaving Ash and his friends trapped by Team Galactic.
Looker and Team Rocket, now disguised as Galactic Grunts, proceed to take over the entrance to the Spear Pillar. Team Galactic leaves their headquarters 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 Galactic Grunts, pretend to stand guard at the entrance with the intent of ambushing Team Galactic just as their chopper arrives and sets down. However, Cyrus and his Commanders easily see through the disguise 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 the Red Chain fragment in his hand, opening the pathway. The path lights up, leading down to the Spear Pillar as Cyrus and his men, except for Jupiter, head inside. Moments later, as Jupiter grows bored of having to wait, Skuntank gets hit by a Giga Impact from Cynthia's Garchomp. Cynthia confronts her as Garchomp restrains Jupiter. Cynthia frees Ash and his friends, locking down Jupiter and the 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 his men reach their destination, placing the Adamant and Lustrous Orbs, as well as the lake guardians, in position around the ancient ruins. 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 mystical energy portals. As the portals begin to take shape, their powers are quickly causing disturbances around Mt. Coronet, which Professor Rowan and Gary pick up from their lab. Dialga and Palkia start to appear at the Spear Pillar, the Red Chains quickly taking control of both. Pikachu, Piplup, and Croagunk fly in on Staraptor, Garchomp, and Gliscor, destroying the cannon. Saturn sends out Toxicroak, but Croagunk jumps from Gliscor and, just as Toxicroak finishes emerging from its Poké Ball, strikes it with Brick Break to the head. Toxicroak falls to the ground, knocked out, to Saturn's shock, while Brock commends a happy Croagunk on a great job.
Though Cynthia is awed to meet the lake guardians, she never wanted to see them this way. Mars sends out Purugly and the Grunts send out Golbat, but Pikachu and Piplup easily put them down, 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 disappear and it appears that Cyrus has lost; however, it emerges that he has a back-up plan—Cyrus summons more power from the Red Chain, and the formations begin to glow, causing Dialga and Palkia themselves to appear. The Pokémon strain under the power of the Red Chain as it takes control of them.
The lake guardians Pokémon draw 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, the effects causing massive disturbances around Mt. Coronet. 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 blocks the attack.
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 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 disappears.
However, Dialga and Palkia continue to rampage, 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 pleads with Ash and his friends to do what they can. One by one, the lake guardians use their energies to calm Dialga and Palkia before creating a portal that sends them back to their isolated dimensions, reversing the energy levels and clearing the area around Mt. Coronet.
The lake guardians celebrates with Ash and his friends before disappearing. Back at the surface, Professor Rowan and Gary arrive. The Adamant and Lustrous Orbs are secured as Gary decides to take them back to Professor Carolina. While Team Rocket makes their getaway, the police take away Saturn, Jupiter, and Mars. Cynthia thanks Ash and his friends for saving Sinnoh as they continue on their journey.