In Alien Abduction, the Alien Pilot and the Alien Co-Pilot serve as commanders of the alien spaceship that abducted The New Kid. The New Kid manages to break free and made his way to the cockpit, where he encounters the pilots. When the Alien Pilot reaches a low amount of HP, he runs away leaving his hat behind, causing the Alien Cockpilot to put on the hat and activate an attack named 'So Be It'. When they are defeated, the U.F.O. loses control and crashes to Earth, causing the green goo to leak out of it and into the drains of South Park.
The Alien Pilots wear blue uniforms and wear pilot caps. The pilot can be distinguished with a winged badge on the pilot cap.
- Shields Up - Controls the Alien Defense Matrix at the start of the battle, which in turns provide Defense Up to the pilots every turn.
- Alien Ray Gun - The pilot fires their weapon once.
- Fire Phasers - The co-pilot fires their weapon three times for moderate damage.
- Fire Photon Torpedo - Remotely fires a fiery torpedo on the New Kid for heavy damage. Inflicts Burning if not blocked.
- Set to Stun - Provides Attack Up to both pilots.
- Set to Stun - Provides another stack of Attack Up to the pilots.
- You Have the Bridge and Make It So - When the pilot reaches low health, the pilot retreats, putting it out of battle, while the co-pilot assumes the new position.