Magneton made its debut as a Magnemite in A Complex Problem!, where it was one of the wild Pokémon living in the Virbank Complex that was affected by the fumes being produced there, causing it to be very aggressive and attack anyone that came near.
It battled Nate in this aggressive state and nearly defeated Turtwig. However, Nate switched Turtwig for Solosis, who confused Magnemite with Confuse Ray and defeated it with Psychic. After the group had managed to stop the fumes, Magnemite, grateful to Nate for helping it, decided to join his team.
In A Shocking Wish!, Magnemite was used to help train a wild Joltik so that it could evolve. It allowed its electrical power to be used by Joltik to boost its own Electric-type moves. After the Joltik had evolved into Galvantula, Magnemite had a brief battle with it.
Magnemite battled several Team Plasma grunts in Ship Shape Rescue Mission! and Battle in the Open Skies!, alongside Turtwig and Duosion.
In A Twist in the Tale!, Magnemite was sent out to battle Kai, who was attempting to steal a Plume Fossil from a researcher working in Twist Mountain. During the battle, Magnemite evolved into Magneton and defeated Kai's Houndoom with Magnet Bomb.
In A Magnetic Attraction!, Magneton was sent out to battle Mag's Nosepass. The two Pokémon were very evenly matched, which only heightened their battling spirits. The intense magnetic field being given off by the two Pokémon reacted with that of Mt. Coronet and caused the two to evolve into Magnezone and Probopass, respectively. Using its new Zap Cannon attack, Magnezone was able to counter Probopass' mini-noses and defeat the Compass Pokémon with Magnet Bomb.
Not much is known about Magnemite's personality. It seems to be quite reserved, as well as apologetic, as seen in its debut where it apologised to Nate for attacking him, despite the situation not being its fault. Magnemite is also more than willing to help others, even allowing a wild Joltik to absorb its electrical energy to help it grow stronger. Its personality remained the same as it evolved into Magneton and eventually Magnezone.