Red, who snuck onto the ship, was quickly surrounded by Magnemite, Voltorb and Electrode, until Lt. Surge came. Since Red escaped, Lt. Surge had Magnemite float around the ship to find him.
Bill showed a picture of Lt. Surge and Magnemite, reminding they were the part of Team Rocket. He pointed this to the Pokémon Association, as they needed some plan to prevent such people from joining the criminal organizations.
Lt. Surge sought Morty, having his Magnemite bind his arm to Ecruteak City's Gym's door. Once Morty and Lt. Surge calmed down, Magnemite freed Morty's arm.
Since Electabuzz was too exhausted to battle, Lt. Surge swapped it with Magnemite, who took Morty's Misdreavus's Psybeam. To finish, Magnemite fired Zap Cannon, which defeated Misdreavus. However, before Misdreavus fainted, it used Destiny Bond and upon being defeated, Magnemite fainted as well.