In the special episode "The Mastermind of Mirage Pokémon," Professor Samuel Oak serves as a pivotal character after receiving Dr. Yung’s invitation to preview a groundbreaking battle system that generates data-based Mirage Pokémon. Oak attends the demonstration with Ash Ketchum, Misty, Brock, May, and Max at Dr. Yung’s laboratory castle.

There, he observes the system reviving extinct Pokémon—Kabutops, Omastar, and Armaldo—and identifies the technology as a completed "Mirage Field," explaining its mechanics. When a masked "Mirage Master" hijacks the system, Oak is captured alongside Dr. Yung. The Mirage Master demands Oak’s research database password, which he defiantly withholds despite threats.

Imprisoned, Oak learns of the Mirage Master’s scheme to forge an ultimate, weakness-free Pokémon using stolen global data, including Pikachu’s extracted information. Oak condemns the plan for disrupting nature’s balance but yields the password "REDGREEN" to halt Pikachu’s suffering during data extraction.

Oak had prudently brought his Dragonite to the event. It battles the Mirage Master’s creations, including a formidable Mirage Mewtwo, but cannot overcome them. His scientific insight and ethical opposition to artificial Pokémon enhancement define his involvement throughout the conflict.