The heroes rush to the Lake Trio, but get bounced back by Skuntank's and Purugly's Iron Tail. Toxicroak uses Sludge Bomb, which bounces off the Pokémon, though the heroes get them. The heroes notice that the Trio is not reacting, as Cyrus has the power of the Red Chain to bind them to his will, using it to shape a new world. Cyrus goes away, putting Saturn in charge to distract the children. Meanwhile, Team Rocket and Looker plan to get in and contact Cynthia. Jessie sends Yanmega, who uses Silver Wind.
The heroes got imprisoned as Team Galactic goes to Mt. Coronet, as they plan to use them should the Trio get out of control. Cynthia sees the helicopter passing and goes towards there. They land near the Gateway and Skuntank uses Flamethrower on some Team Galactic members, which are Team Rocket and Looker, as the disguises are off and are imprisoned with the heroes. Using the key, Cyrus touches the door and the ruins are open. The ball lightens the way and they go in, except Jupiter. Cynthia's Garchomp uses Giga Impact, hitting Skuntank and binding Jupiter. Soon, Cynthia frees everyone.
Jupiter is imprisoned and the heroes go in the ruins, though Team Rocket have reached the Spear Pillar. With the Trio on the pillars, the Adamant and Lustruous Orbs in place. The Red Chain is fired, as two portals are opened. Cyrus calls on Dialga and Palkia, and as they are summoned, the Red Chain binds them. However, Pikachu uses Thunderbolt, and the machine is destroyed. Saturn sends Toxicroak, but just before it is out, Croagunk defeats it with Brick Break. Mars sends Purugly and some members send Golbat. Pikachu's Thunderbolt and Piplup's BubbleBeam stop them, however.
Pikachu, Piplup and Croagunk shatter the gems on the Lake Trio's heads and they are out of Cyrus' control. This causes Dialga and Palkia to disappear. Ash calls Staraptor and Gliscor, whom Pikachu and Piplup rode. Cyrus, however, still controls Dialga and Palkia, through the Red Chain, as the Legendary duo are in pain. The Lake Trio bond with the heroes and ask them to save Dialga and Palkia. Cyrus commands the duo to create a new world; Dialga and Palkia use their power and soon a vortex is created, containing energy in which galaxies are seen. Outside, many disasters happen, as Jupiter knows the old world is being destroyed and a new one is forming.
Cynthia advises the heroes to aim for the chains. Pikachu uses Thunderbolt, Piplup BubbleBeam, Garchomp Draco Meteor and Croagunk Posion Sting. However, Palkia uses Spacial Rend and Dialga Roar of Time. The attack continues, but the Lake Trio use Protect and no damage is done. Mars and Saturn advise Cyrus to get in the new world, but Cyrus does not allow them, as it is his alone and their presence will threaten the new world. Garchomp, Pikachu, Croagunk and Piplup continue their attacks and with the Lake Trio, they shatter the rings around Dialga and Palkia. The vortex is vanishing, so Cyrus steps in and the vortex vanishes, along with him.
Dialga's Roar of Time and Palkia's Spacial Rend cause the world Cyrus is in to be destroyed. However, it makes a portal which suckes everything inside it. The Lake Trio appears again and want to help. Azelf goes in the portal and stops it from sucking everything; Uxie calms down Dialga and Palkia; Mesprit eases their pain from the Red Chain. The Lake Trio makes another portal, in which Dialga and Palkia go into. The disasters are no longer present. Ash asks the Trio why did they choose them, so Cynthia believes it is because they care much about Pokémon. The Trio vanishes, as their work is done.
The Lustrous and Adamant Orb are safe; Gary tells they will send it to Prof. Carolina. Looker does not see Team Rocket; they went in the balloon and cannot wait to report this to the boss. Jupiter, Mars and Saturn are imprisoned, as Team Galactic is no longer present. Cynthia thanks the heroes, as they helped protect the Sinnoh.
- Professor Oak's Pokémon lecture: Beldum
- This is the last appearance of Gary.
- This episode features the most number of legendary Pokémon (Azelf, Uxie, Mesprit, Dialga, and Palkia).
- Darkrai and Giratina replace Palkia and Dialga in the opening scene.
- Music from Pokémon Heroes, Lucario and the Mystery of Mew, The Rise of Darkrai, and Giratina and the Sky Warrior is used in this episode.
- When Uxie, Azelf, and Mesprit use their abilities on Dialga and Palkia, Uxie's visually resembles the powers of Sheena and Damos to read Pokémon's hearts.
- When the Red Chain puts the rings around Palkia and Dialga, they resemble the rings of Arceus.
- A preview of future episodes is also shown. These include in order of the preview:
- Ash's Gliscor learning Giga Impact (Mastering Current Events!),
- Ash's Buizel learning Ice Punch (Short and to the Punch!),
- Dawn's Flame Ice combination with Mamoswine and Cyndaquil (Double-Time Battle Training!),
- Zoey appearing, with a Leafeon and Kirlia (Double-Time Battle Training!),
- Barry appearing (Gotta Get a Gible!),
- Ash obtaining a Gible (Gotta Get a Gible!),
- Ash's Gible battling with Barry's Empoleon (Gotta Get a Gible!).
- Team Rocket doesn't blast off or recite their motto in this episode.
- In a scene, Uxie, Mesprit, and Azelf float in front of Brock, Dawn, and Ash in that order; in the very next shot, Uxie and Azelf have switched positions.
- In a scene several minutes later, the same occurs, with Azelf and Mesprit switching positions.
- Near the end of the episode, the tail of Team Rocket's balloon is missing.