Pirate Commander

A Pirate Commander is a high ranked Space Pirate found in Metroid Prime 3: Corruption. A Space Pirate can only become a commander if they were a Commando Pirate for at least 10 years. They wear Red Phazite armor, which is very rare and much more resilient than usual Phazite armor. The Pirate Commander appears multiple times on the Homeworld before the fight, displaying the ability to summon multiple Pirate Commandos and to teleport. Both abilities are also displayed during the battle. On the "Pirate Homeworld", he shows up repeatedly to summon more pirate commandos and impede Samus' path. During Fleet Admiral Dane's assault on the homeworld, two Federation Marines can be found firing down a hallway to the left of Samus. If Samus watches long enough, the commander will show up and slash through both of them, killing them instantly.

An Echoes-style Commando squad was led by a Space Pirate wearing modified Commando armor in the Episode of Aether manga. Since Commanders are refered to as ex-Commandos, this was likely an early appearance of a Commander before the Phazite armor was implemented.

Battle
The Pirate Commander will generally summon 4 Pirate Commandos at once and warp around the arena causing havoc. When the Commandos are killed the Commander will summon more up to a certain point when no more are called. Due to his constant teleportation, he is difficult to attack. Samus's best weapon against him is Hypermode-all of her other weapons will have very little effect. Unlike Commandos, he cannot be killed with a headshot from the Nova Beam.

Logbook Entry
Metroid Prime 3: Corruption: "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."