Musashi operates within Team Rocket, relentlessly pursuing both Arceus and the Jewel of Life across the film. The team functions independently, driven by their ambition to seize Arceus and steal the Jewel of Life for personal gain.

When Arceus devastates Michina Town, Team Rocket takes refuge within crumbling ruins to survive. Sheltering there, they uncover several ancient artifacts, mistakenly believing them to be priceless treasures including crowns and a tiara. Contextual scenes set in the past later expose these items as mundane objects: a cooking pot and a Cyndaquil harness.

Musashi critically advances the plot by finding the genuine Jewel of Life during the past timeline, a discovery essential to resolving the conflict. Team Rocket's involvement concludes as the collapsing temple during Arceus's present-day judgment sweeps them into a river.