In *Pokémon: Jirachi Wish Maker*, Jesse operates as a Team Rocket member alongside James and Meowth. During the Millennium Festival celebrating the Millennium Comet's arrival, the trio adopts clown disguises to distribute flyers for "The Great Butler's Magic Show". Their undercover duties include promoting the show and shoveling manure.
Seizing the moment during Butler's magic performance, Team Rocket abandons their clown outfits. They descend into the tent via balloon, capturing Pikachu along with Butler's Kirlia and Mightyena inside an electricity-proof container. Jesse announces their plan to make the Pokémon "disappear". Butler's Dusclops intervenes, freeing Pikachu with Will-O-Wisp. Ash then commands Pikachu to strike Team Rocket with Thunderbolt. Dusclops follows with Night Shade, blasting them from the tent.
This intervention during the magic show marks their sole contribution to the film's events; they play no further part in the unfolding story involving Jirachi, Butler, or the false Groudon crisis.