Arceus's Judgment rains down the sides of Mount Coronet, striking Team Galactic's helicopter. While the Commanders and their pilot Grunt jump off with parachutes in time, they and their Pokémon are quickly bound to a rock by Cynthia's Roserade's Power Whip and forced to watch as the space-time gate they worked so hard to open closes, returning the sky to normal.
However, the lava monster Heatran is still close to exploding, threatening the entire Sinnoh region. Ash and his friends plead for Arceus to help, and it accepts their pleas. As the lava monster grows more and more unstable, Arceus reveals its Plates and uses one of them to transform into a Water type, before forming an entire ocean in the sky, amazing everyone with its power. Ash warns Arceus that their earlier attempt to use water on Heatran didn't work, but Arceus simply nods to signal that everything is fine. Wanting to do something to rescue the real Heatran as well, Ash figures that they need to use both water and fire. Goh, having gotten used to Ash's improvisational skills, agrees to follow his lead, while Dawn is initially sceptical, but with some motivation from Piplup, agrees to follow him as well. Brock and Cynthia, meanwhile, agree to stay behind to provide backup.
Arceus pours down the sea it's created in the sky, forming it into a dome of water around Heatran to contain it. Brock notes that unlike before, the meeting of fire and water isn't causing an explosion, which Cynthia explains as a demonstration of how Arceus's power can even overturn the laws of nature. The lake guardians grab Ash, Dawn, and Goh into a Psychic hold and carry them into the water dome. Once inside the dome, Dawn has Piplup use Whirlpool, which Ash has Pikachu coat with a Thunderbolt before it's released at Heatran, trapping it. Goh then carries on the plan by having Inteleon use Snipe Shot, penetrating into the very core of the lava monster. The group dives through the tunnel, reaching the space where the real Heatran is trapped, right next to the unstable Flame Plate. Pikachu cuts Heatran free with Iron Tail, while Goh has Cinderace use Pyro Ball to coat the Lava Dome Pokémon in flames. Finally, Pikachu finishes the insulation with an Electroweb.
With Heatran in Uxie's Psychic tow, the group starts heading out as the Flame Plate causes the lava monster to be driven closer and closer to an explosion. The increasing pressure blasts Ash and his friends into the water dome, where the coating around Heatran falls off, causing it to start sinking. The group quickly flies over to Heatran and starts pulling it. With the lake guardians' help, they soon make it out of the dome and land safely on the Spear Pillar. Moments later, the lava monster finally explodes completely, but Arceus's power keeps the explosion contained. The Flame Plate emerges from the explosion, and Arceus reclaims it as Heatran recovers and stands up.
Ash and his friends thank Arceus and the lake guardians for their help. As the four Pokémon begin ascending towards the sky, the Team Galactic Commanders plead Arceus to tell them where Cyrus is, but they're given no response. Watching Arceus disappear into the sky, Cynthia speaks of how Arceus wishes people and Pokémon to overcome adversities together, appearing to provide them a hint if they face a hardship too difficult to surpass so the problem can be solved, as they must overcome their adversities on their own, hence why it had left the actual task of saving Heatran to them. As the Sinnoh Police, led by Officer Jenny, arrives to arrest Team Galactic, Brock tries to ask Cynthia out for a date, only to be brought down by Croagunk's usual Poison Jab, much to Goh's surprise. With a new day dawning over the Sinnoh region, Ash and Goh are happy with how eventful their research trip ended up being, and Ash shares a high five with Dawn. Below them, the frozen remains of the lava monster stand on the mountainside.
In the past, Rei runs to his house in Jubilife Village, crafting himself some Poké Balls before setting out to explore the wilderness of ancient Sinnoh with his partners Rowlet, Cyndaquil, and Oshawott. Above him, Arceus gallops across the sky towards the summit of Mount Coronet.