Magneton debuted in Clemont's Got a Secret. It served as a patrol for the Gym. After Ash defeated Magnemite with Froakie's help, Magneton appeared and attacked the group with Metal Sound. Serena's Fennekin battled Magneton and attacked with Ember, which Magneton easily dodged by temporarily separating itself into three. Despite having a type-disadvantage, Magneton overpowered Fennekin and Froakie came to the rescue by stopping it with its Frubbles.
After Clemont had his battle with Clembot to determine ownership of the Gym, Magneton cheered along with the group and Clemont's other Pokémon when Clemont was able to reprogram Clembot.
Magneton is very loyal both to Clemont and Clembot, albeit to a fault, as shown when Clembot's orders for it to attack any intruders led to it attacking Clemont, also demonstrating how it takes orders from either of them very seriously. It has the ability to split itself into three separate units, and it utilizes this talent to evade oncoming attacks.