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Cobalion is first seen talking to his main minions and showing them the power of the Glowdrops, to destroy rust, with Toy Town's Glowdrops. Cobalion is later seen at the Great Glowing Fountain. He battles the player in a 1 on 3 Team Battle. When the player is defeated, Cobalion will send them flying, and, coincidentally, the player lands in Easterly Town, where Cobalion is stealing Easterly Town's Glowdrops. At the end of the third chapter, Chapter 3: Tracking Cobalion, Cobalion attacks the player, twisting the player's Wonder Key, making the key a Bent Key. This can be undone by earning the Temple Key from the Temple of Keys's Battle Royale.
When Cobalion is met next, at the end of Chapter 4: The World Axle and the Secret of the Wonder Key, he is giving a speech to his minions. When he sees the player and Golett, he says "We knew there would be sacrifices!" and challenges the player to another 1-on-3 Team Battle. When Cobalion is defeated, his minions are "Rusted" by Dark Rust. They and Dark Rust retreat into the World Axle. Cobalion and the player then team up to fight Dark Rust. In Dark Rust's Fort, Cobalion sacrifices himself to destroy Dark Rust's barrier and its ability to create a barrier.
When Terrakion and Virizion have been defeated, a Rusty Cobalion appears, as if defeated. When it is picked up, the message "This Cobalion toy has seen better days. Take good care of it." will be shown. All of Cobalion's followers call him "the leader" or "lord Cobalion".
