Musashi operates alongside Kojiro and Meowth as Team Rocket, infiltrating the research team employed by Dr. Zed at the Biotope Company, which studies the Forest of Okoya. Their covert presence within the organization enables them to gather intelligence on Zed's activities and motives. Team Rocket discreetly maintains their cover within the research group while observing events involving Koko, Ash, and Zarude.

The trio exhibits visible horror upon discovering Dr. Zed's responsibility for the deaths of Koko's human parents. Despite their typical antagonistic focus on stealing Pokémon, particularly Pikachu, they demonstrate ethical boundaries in this instance, shifting from self-serving opportunism to facilitating justice against Zed.

During a critical moment when Ash and Pikachu are captured by Zed, Team Rocket deliberately engineers Pikachu's release from confinement. This decision is strategic, recognizing that freeing Pikachu creates an opportunity to obtain a keycard needed to access restricted areas within Zed's operations. They prioritize this tactical advantage over an immediate chance to capture Pikachu, calculating that future opportunities to steal the Pokémon would arise.

Following Dr. Zed's defeat, Team Rocket anonymously delivers incriminating evidence of his crimes to the authorities. This action directly results in Zed's arrest and subsequent imprisonment. Their choice to expose Zed, despite gaining no tangible benefit and operating outside their usual criminal objectives, underscores their rejection of his extreme actions against humans and Pokémon.