Jessie operates alongside James and Meowth as Team Rocket, focused on capturing Arceus and seizing the Jewel of Life for their organization. She witnesses Arceus's dramatic arrival and the resulting devastation at Michina Town's ruins. Amidst the destruction following Arceus's attack, Jessie spots the true Jewel of Life concealed within Marcus's staff, recognizing it after learning Sheena carried a counterfeit.

Team Rocket devises a scheme to steal both Arceus and the genuine jewel, dubbing their plot the "Joy of Double Prizes." Their attempt is abruptly halted when Arceus shatters the ruins, sending Jessie, James, and Meowth plunging into the river below and foiling their immediate plan. Following Ash and his friends' successful intervention in the past, the altered timeline causes the real Jewel of Life to vanish from Team Rocket's possession in the present.

Separate from the jewel pursuit, Jessie, James, and Meowth engage in an attempt to steal watermelons, echoing their past comedic misadventures. Jessie also reacts with excitement upon seeing Dialga and Palkia appear alongside Sheena, expressing her awe at witnessing the legendary Pokémon and her abilities, though her focus remains firmly on leveraging the situation for Team Rocket's objectives.