Team Galactic has taken over the Iron Island ruins, where their Spear Key has unleashed a strange energy from the ruins. On top of that, the frequency from their machines has driven the local Steel-type Pokémon berserk! The energy has overwhelmed Riley's Lucario, and Lucario attacks Riley and our heroes. Fortunately, Riley is training to be an Aura Guardian, and he uses his own Aura to shield everyone. At Riley's insistence, Pikachu hits Lucario with a Thunderbolt—Lucario backs off, but then it charges Team Galactic! In the meantime, the energy from the ruins has triggered reactions from distant Mt. Coronet and even the meteorites in Veilstone City, and scientists around the region are scrambling to figure out what's happening.
Back on Iron Island, Commander Mars' Purugly defeats Lucario, but Riley realizes Lucario was trying to destroy Team Galactic's machines. As our heroes run to finish what Lucario started, Piplup falls into the same cavern where Barry and Team Rocket were trapped after their own scrap with Team Galactic. When Dawn tries to help get them out, an angry Steelix knocks her into the cavern! Riley holds Steelix at bay while Ash and Brock finish the mission; as soon as Pikachu destroys Team Galactic's machinery, Steelix and the island's other Steel-type Pokémon calm down.
This also shuts down the ruins, so Team Galactic beats a quick retreat. As a parting gift, they wire the ruins with enough explosive to blow up Iron Island. Riley and Lucario run to disarm the bombs, but Ash and Brock need to rescue their friends from the cavern. James' Carnivine comes to the rescue: it uses a new move, Vine Whip, to help pull itself to the surface, then pulls up everyone else. As our heroes rejoice, Commander Mars, now a safe distance from the island, hits the detonator for the explosives. The whole island trembles, but remains intact!
Riley and Lucario used their combined powers of Aura to contain the detonating bombs and channel them high above the island to explode harmlessly. With everything quiet for now, Cynthia's grandmother Carolina flies in to examine Team Galactic's handiwork. Both the ruins and Team Galactic's machine are made of the same compound as the Veilstone meteorites; Team Galactic must be using that to locate Spear Pillar, a key to summoning Dialga and Palkia. Riley offers to help Carolina survey the island, but Ash and his friends have other things on their mind. They part on friendly terms with Barry, then get on the ferry. Their destination: Dawn's next Contest and Ash's next Gym battle!