The Alien Commander pilots the Alien Mothership, has a red cape and its brain is visible. It has the same shape of head as the Alien Cyborg, and the same shape of legs as the Squid Warrior, except that they are reversed. The left eye has a long streak across it; probably resembling a scar or a mark. It also has golden epaulettes, as seen on soldiers from the Pirates theme, and its head is made up of three parts. He follows the orders of the High Command.
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- In a movie on the Alien Conquest website, the Alien Commander is laughing while alien ships fly toward Earth.
- He has a pet Alien Clinger that is named Captain Ploovie.
- He is the only alien to date to have a cape and epaulettes.