Ash and his friends have arrived in Oreburgh City to investigate the strange disturbance that their Pokémon felt. They are struck by a sudden ear-splitting sound, which turns out to be caused by a fight between a group of Chingling and a Bronzong, which are all going crazy. Dawn has Piplup use Whirlpool to douse them, calming them down and stopping the fight. However, as the group approaches the injured Pokémon, they suddenly find themselves in a strange space, where Azelf, Uxie, and Mesprit appear before them, showing the group a vision of a sea of flames. Arceus appears above them as well, but just as suddenly as the strange vision started, it, the lake guardians, and Arceus disappear. Goh is baffled at how Ash and Dawn are so calm after what they just saw, until Ash explains that back when he and Dawn were adventuring through Sinnoh together, they and the lake guardians rescued Dialga and Palkia together. Goh is amazed to learn this, but the group quickly refocuses on getting the injured Chingling to a Pokémon Center.
At the Team Galactic HQ, Saturn makes an announcement to all the Team Galactic Grunts. Back when Team Galactic tried to create a new world, their leader, Cyrus, had Dialga and Palkia open a space-time gate. But when his plans were foiled, he had jumped into the vanishing gate and disappeared. Now, thanks to Heatran's power, all preparations are complete, and Team Galactic is ready to open a new space-time gate and bring Cyrus back. Saturn orders the Grunts to prepare for the start of the operation at 6 p.m.
At a Pokémon Center, Ash and his friends watch television news regarding the cases of Pokémon acting strangely, all of which seem to have occurred with Pokémon living on Mount Coronet. They're approached by a doctor telling them that the Chingling they brought is getting better, and it turns out to be none other than Brock. Ash and Dawn are excited to see their old friend again, while Goh is thrilled to meet him for the first time, having heard from Ash that he's a former Gym Leader and Pokémon Breeder, who's currently training to become a Doctor. Ash is surprised to see Brock being accompanied by a Blissey, whom Brock confirms to be the evolved form of the Chansey that he raised from a Happiny, as well as his current assistant, along with his Croagunk. Having heard the news, Brock agrees to accompany the group to Mount Coronet, taking them aboard a flying craft that he uses for house calls. Along the way, they tell him about the vision they saw, which Brock realizes could've been a message sent not by the lake guardians, but by Arceus. Realizing that Brock is right, Dawn decides to call Cynthia with her Pokétch so she can come help them.
Team Galactic commences their operation, deploying an energy cannon on the rooftop of their headquarters and aiming it at the sky above Mount Coronet. Saturn commands Heatran to use Magma Storm on the Flame Plate, filling it with immense energy that is fed to the energy cannon and fired into the sky, where it begins to open a space-time gate. The beam is noticed by Ash and his friends, who head towards it. The gate gradually expands, but in his enthusiasm of being about to bring back their leader, Saturn has Heatran fill the energy cannon with too much energy, causing the energy flow to turn backwards and strike Heatran. A massive explosion tears a section of the Team Galactic HQ apart and stops the energy beam. Heatran emerges from the rubble, covered in flames and roaring wildly. Saturn attempts to recall Heatran, but the intense flames around it cause him to drop Heatran's Dusk Ball, which melts in the Lava Dome Pokémon's scorching presence. Team Galactic begins an evacuation, during which Heatran walks towards the Flame Plate and swallows it whole, becoming completely engulfed in flames as a result. Saturn figures that Heatran's Flash Fire Ability must've been overloaded by the power of the Plate, causing it to go berserk and assume its current form.
Heatran fires a beam of energy at the space-time gate in the sky, before starting to move towards it, setting a forest ablaze as it lumbers through it. The Legendary Pokémon is spotted by Ash and his friends, who realize that the flames they saw in their vision were those of Heatran. The Team Galactic Commanders, pursuing Heatran on a helicopter, theorize it's headed for the Spear Pillar. Saturn is delighted by this, but his attention is focused elsewhere when he spots Ash and his friends approaching Heatran as well. The group also realizes that Heatran's destination could be the Spear Pillar, and given that it was where Team Galactic enacted their big plan, they suspect the villainous team being behind this incident as well. They cut ahead of Heatran and prepare to put out the flames surrounding it with their Water Pokémon, but Brock says the fire is too intense and they have to figure out another plan.
Suddenly, the group is attacked by Saturn's Toxicroak, causing Brock's Croagunk to emerge from his Poké Ball at the presence of his rival. Team Galactic's helicopter lands before them and the Commanders hop out of it, confirming the group's suspicions. Brock questions how could they be here, since Team Galactic was dismantled by the Sinnoh Police, but the Commanders refuse to explain that or what they're planning to do with Heatran. Arceus reacts to the Flame Plate inside Heatran, and the lake guardians appear near the group again. The Legendary trio flies over Heatran, trying to calm it down. In response, Heatran roars and sheds its coat of flames, revealing a new form made entirely of molten lava.