Red Eyes first appears at the start of the game, shooting the player with his Z.Z. Flyer. He appears again at Rasp Cavern, where he steals Raikou's Emblem from the Involith. Red Eyes is responsible for the damage to the Big Booker Bridge using Electrode in an attempt to stop the player following him. Later, he contacts the player and Murph to offer to exchange Blue Eyes for the player's partner at Daybreak Ruins, where he steals Entei's Emblem in the involith. Red Eyes appears again at Faldera Volcano, where he tries to awaken Moltres and battles the player with a Charizard. He appears again trying to awaken Articuno on Mt. Sorbet, he challenges the player with a Typhlosion. Once Red Eyes is defeated, he leaves, his pride shattered. After the credits, during Supurna's mission, he appears in the sky, and, holding the last piece of Edward's Golden Armor and he challenges the player with a Blaziken on Mt. Sorbet for it. In his last appearance, during a quest, Red Eyes appears and hands the protagonist 2 out of 3 monument parts from the Involiths.
Cranidos was controlled by Red Eyes in an effort to prevent Ben from interfering in the plans of the Pokémon Pinchers. It proved its strength by defeating the Ukulele Pichu with a powerful Headbutt. However, Cranidos was clearly not acting under its own will, and it was quickly returned to normal thanks to Ben's Capture Styler.