"Pokémon: Gear Heart of Rust Town" tells the story of the trainer Azhe and his partner Metal Monster who were led to the abandoned Rust Town by a mysterious flyer during their journey, and thus became involved in a series of secrets and agreements that spanned time and space.
The story begins in the ruins of Rust Town. Azhe discovers that the gear Pokémon here behave abnormally. There are hidden secrets affected by the energy of red crystals deep in the bell tower and mines. In order to protect the townspeople, the giant gear king locked the crystals with himself but fell into control. After solving the crisis in Rust Town, Azhe's journey continued. He encountered a change in the energy of the lighthouse in Liulic Port, and discovered that the red crystal was related to the gear navigator, the mechanic and the young Gear King of the shipwreck three hundred years ago. Later, in the Hidden Mist Swamp, he encountered the Iron Anchor Dragon controlled by Rust Spores, revealing the past that Rust Town, Liulic Port, and the swamp formed an energy system through a metal mesh.
Along the way, Azhe continues to unravel the mystery of Pokémon mutation, witnesses the persistence of Pokémon such as Gear King, Tide Gear Monster, and Anchor Dragon in sticking to the agreement, and gradually understands that behind these connections spanning three hundred years is the unbroken bond and protection between Pokémon and humans.