Aipom and Buizel are battling in a field when Aipom deflects Buizel's Sonic Boom into an old stone tower, knocking it down. Then the skies darken and a Pokémon emerges from the ruined tower: Spiritomb! Spiritomb flies off, causing havoc wherever it goes—first it wrecks Team Rocket's dinner, then it wrecks an entire village!

One of the villagers is an old lady who knows this damage is the work of Spiritomb. Long, long ago, Spiritomb caused trouble for the villagers until an Aura Guardian and his Pikachu sealed Spiritomb inside a Hallowed Tower made of stone. That sounds an awful lot like the tower our heroes accidentally knocked down! Ash and his friends promise to make things right, they're approached by Team Rocket, who are disguised as psychics. They pretend to help calm Spiritomb down, but then spring a net over Pikachu and Spiritomb.

Spiritomb blasts the net apart and chases down Team Rocket. But Meowth discovers that Spiritomb is really looking for revenge on the Aura Guardian who sealed it in the Tower. Meanwhile, our heroes need to stop Spiritomb, so they lure Team Rocket into a trap and Spiritomb is close behind. But when Team Rocket tells Spiritomb that Ash is a descendant of the Aura Guardian, it turns its wrath on Ash!

With Spiritomb in hot pursuit, Ash runs to the ruins of the Hallowed Tower, yet Spiritomb is too powerful to be sealed away. Pikachu is exhausted, but as clouds gather overhead, Ash gets an idea. Pikachu uses Thunderbolt on the skies, attracting a lightning bolt that fills it with energy. Then Pikachu defeats Spiritomb and the wayward spirit is sealed back into the Hallowed Tower, this time for good!