After having traded, Ash and Dawn decide to get used to their new Pokémon. After a few minutes of battling Ash's Buizel uses SonicBoom which is then deflected by Dawn's Aipom's Focus Punch and sent into a Hallowed Stone Tower. The tower immediately crumbles into bricks. The bricks of the Hallowed Stone Tower then begin to glow. The sky turns black and clouds roll in. In the rubble lies an Odd Keystone.
Lightning strikes the keystone and from it emerges Spiritomb who then proceeds to attack the group with Shadow Ball and Hyper Beam. The group try to counter with Buizel's Water Gun however the attack goes straight through Spiritomb. It then responds with Shadow Ball knocking Buizel out. Spiritomb then flies away. Soon after, it encounters Jessie, James and Meowth and attacks them with Hyper Beam and Dark Pulse. It then flies away hitting Jessie's head with its Keystone in the process.
The next day Ash and his friends arrive in the village to find it derelict. They hear stories about a strange Ghost-type Pokémon that attacked the village in the night. They immediately connect this with Spiritomb. They meet an old woman who tells them the story of Spiritomb which terrorized the village and how an Aura Guardian with a Pikachu defeated and sealed away Spiritomb in the Hallowed Stone Tower 500 years ago. Then the group realizes they've destroyed the same tower and takes the old lady to it who acts furious seeing it. Then they apologize promising to make things right.
Then Team Rocket shows up disguised as psychics. Jessie pretends to be saying facts that happened in their past life, while James tells them that Meowth (who is disguised as a Sneasel) has the ability to communicate telepathically with other Pokémon. Next, the old man's grandson appears informing them of Spiritomb's return. They return to the village where Meowth uses "telepathy" to communicate with Spiritomb. Meowth returns and whispers into James's ear that Spiritomb wants something from Pikachu. Jessie takes Pikachu to Spiritomb and throws a net over both of them revealing their identity. After reciting their motto they take off in their balloon.
Spiritomb uses Ominous Wind, which slashes Team Rocket's balloon and making them crash to the ground. It then lets itself free, to which Jessie sends out Seviper but it is quickly knocked by Spiritomb's Hyper Beam. Then Team Rocket flees with Spiritomb following them. Spiritomb catches up with them, revealing to Meowth it wants revenge on the Aura Guardian for sealing it in the Keystone. Knowing the Guardian lived 500 years ago they flee again with Spiritomb on their tracks.
The scene turns to the group searching for Spiritomb. Dawn realizes Spiritomb gave chase to Team Rocket and makes a plan in order to lure them. The scene reverts to Team Rocket in their balloon. They notice Pikachu alone, sleeping in a meadow. They land and head for Pikachu but they get into a pitfall trap. Then the group proceeds to imitate Team Rocket's motto but are interrupted by an angry Jessie.
Spiritomb shows up and Team Rocket convinces Spiritomb that Ash is a descendant of the Aura Guardian. It turns its anger on Ash and attacks him with Hyper Beam. Ash dodges and agrees to battle it. Ash runs to the ruins of the Hallowed Tower with Spiritomb in close pursuit. It stops Ash and Pikachu in their tracks by using Dark Pulse. Pikachu replies with Quick Attack but Spiritomb dodges. Then Pikachu uses Thunderbolt hitting Spiritomb which counters with Hyper Beam.
They start running again but Spiritomb stops them. Pikachu continually uses Thunderbolt getting more and more tired while Spiritomb resists each attack. Then it uses Shadow Ball but misses Pikachu and hitting Team Rocket blasting them off. Then it initiates in a Giga Impact striking both Ash and Pikachu. Pikachu falls on the ground exhausted as clouds gather above. Ash urges him to stand up and to send a Thunderbolt up towards the sky which re-charges Pikachu's energy. Pikachu uses Volt Tackle, then Thunderbolt defeating Spiritomb. The group then seals Spiritomb away in the Keystone. Then the old lady invites them for dinner.
In the end, the scene cuts with the narrator's conclusion.