Butler was assigned by Team Magma to bring a Groudon back to life using a fossil of the prehistoric Pokémon. Unfortunately his experiment failed as his machine lacked the proper amount of power. This got Butler exiled from Team Magma, and was the sole event that caused his hatred to boil and to seek revenge on the organization. Butler then planned to use the power of the millennium comet to complete his experiment, and was in need of a Jirachi which could channel the comet's energy. Some time later, Butler found the Jirachi he had been searching for in the land of Forina.
After the Jirachi had awaken from its thousand year sleep, Butler successfully finished his experiment. Unfortunately, his creation was pure evil and was rogue, devouring everything in the vicinity with gelatinous tentacles expelled from its spikes, including May, Brock, Diane, Jessie, James, Meowth, and many Pokémon. After seeing the error of his ways, Butler decided to aid Ash in destroying his own creation. Butler distracted the Groudon on his Salamence while Ash and Max rode on the back of a wild Flygon to Butler's machine. They barely escape being eaten themselves when Salamence swoops in front of the Flygon. Salamence however doesn't escape and Butler is sent falling to his doom, only to be rescued by Jirachi teleporting him.
Once the group safely arrived on Butler's machine, Jirachi is placed inside and begins charging a powerful attack. This catches the Groudon's attention who begins a full on assault. Ash buys Jirachi some time by getting back on Flygon and distracting the beast. Once fully charged, Jirachi unleashes a Doom Desire and sends the Groudon high in the air where it is then obliterated.
After the Groudon was defeated, all of the people and Pokémon it had eaten were revitalized.
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For more information on this Pokémon's species, see Groudon.