A Pirate Commander is an elite Space Pirate found only in Metroid Prime 3: Corruption. A Space Pirate can only be a Pirate Commander after being a Commando Pirate for at the minimum of 10 years. Commanders wear Red Phazite armor, which is much more resilient against attacks then the normal Phazite armor. They were a personal teleportation device that lets them move around a battlefield quickly and sporadically. When Samus Aran fought one in Corruption, it showed the ability to call Pirate Commandos to its aid.
- "Commanders make heavy use of their personal teleporter, moving to favorable positions and across the battlefield, giving orders and support as needed. They carry all of the weaponry and gear used by commandos, with the exception of their armor, which is forged out of ultrarare Red Phazite. A rare breed, Pirate Commanders have lived to rise to the ruling caste on the Pirate Homeworld. Each has been a commando for at least ten years." — Logbook "Pirate Commander" (Metroid Prime 3: Corruption)