On Iron Island, Ash's rival Barry is training with his Empoleon and Heracross when Empoleon suddenly turns on its Trainer. Barry calls Ash and Dawn, who are still in Canalave Town, to tell them what happened—other Pokémon on Iron Island are acting strangely, too! Ash and his friends catch the next ferry to Iron Island, with Team Rocket following them in secret, but Barry has already gone out to explore the island. Whatever is happening, only Steel-type Pokémon are affected, but why?
Ash and his friends search for Barry and encounter more Steel-type Pokémon running amok. Ash is even saved from an angry Aggron by a dapper Trainer, Riley, and his Lucario. Riley is a Steel-type Trainer who lives on Iron Island, and his Lucario uses its Aura to protect itself from the low-frequency wave that's driving other Steel-type Pokémon mad. Barry and his Heracross, off on their own investigation, spot a strange machine. Barry runs into Team Rocket and promptly blames them for everything, but Team Rocket denies that the machine is theirs. Barry and Team Rocket go to get a closer look, and discover that the machine is part of a Team Galactic operation headed up by Commander Mars!
When Team Galactic spots them, Barry and Team Rocket put up a fight but are quickly overpowered and knocked into an ancient underground ruin. Up on the surface, Riley and our heroes have also tracked Team Galactic to the ruins, which are made of metal. Together with Team Galactic's Spear Key, this must be causing the low-frequency wave! Commander Mars releases the Spear Key and the Key melds with the ruins, which release a huge bolt of energy. The wave of energy knocks Lucario backwards; as it gets to its feet, it's overcome by a strange power and prepares to attack!
Barry's training is going well on Iron Island, as Heracross and Empoleon destroy a rock with ease. Empoleon suddenly get struck down by a low frequency sound wave and becomes aggressive. It then blasts Barry and Heracross with a Hydro Cannon.
Meanwhile, Ash, Dawn and Brock are getting prepared to leave Canalave City to head to Dawn's next Contest in Chocovine Town. Since they are heading up north, Ash adds that they will go to nearby Snowpoint City afterwards for his next Gym challenge. Before they leave, Ash receives a call from Barry asking about how his training is going. Ash shows off his new Badge, affirming his victory at the Canalave Gym. Barry reveals that something is currently wrong with his Empoleon and some other Pokémon who've begun to act violently. Iron Island's Nurse Joy explains that she can't figure out why this is only happening to Steel-type Pokémon. Ash and his friends set their sights on Iron Island next, determined to solve this mystery.
They take the next ferry to Iron Island but when they get to the Pokémon Center, they find out that Barry has already left. While exploring the island, the group find that all the Steel Pokémon are trying to hurt them and themselves. Suddenly, a huge Aggron charge at them, though Riley steps in and has his Lucario use Close Combat to take out the threat. Using his aura, Lucario can detect the waves and if any rampaging Steel Pokémon are nearby, although it will not be affected because he can also use the aura to protect himself from the waves. Afterwards, Riley guides the group to town and says he will find Barry during his continued investigation of the low frequency sound waves. Ash and his friends protest, adding they want to help the Iron Island Pokémon. Riley warns them that it is dangerous and they will have to act without hesitation.
Meanwhile, Barry leaps of a cliff to evade some angry Magnemite. His Heracross steps up and tries to fly Barry through the air, where they spot some odd machinery in the distance. However the pair are knocked to the ground by a Skarmory, landing on top of Team Rocket, who followed the twerps to the island. Barry accuses them of angering the Steel types, pointing out a device he spotted in the air but Team Rocket claim it was none of their doing. He leads them to the location, which turns out to be a Team Galactic base led by Mars. While spying on Galactic's operation, a Steelix knocks them directly into view. Mars promptly summons her Golbat, who knock Heracross out with a fury of Air Cutter. Barry calls out his Roserade and Staraptor, accompanied by Team Rocket’s Pokémon. However the Golbat quickly defeat them all with Air Cutter and Sludge Bomb attacks. Meowth steps up to use Fury Swipes, but Purugly replies with its claws. Barry and the Rocket trio then fall through a crevice into a small cave with Dialga and Palkia etchings.
Ash and friends finally reach the base with Lucario's help. The group informs Riley of Team Galactic’s motives to uncover the Sinnoh timespace legend. Eventually Mars picks up the Spear Key, which fits directly into an etched panel on the ruins. The ruins take on a blue glow and a powerful beam of light is sent out, striking near Mt. Coronet's summit. Even Lucario can't fight the disturbance anymore, and is about to attack the group while Ash and Riley try to calm it down.