Pirate Commandos were a specially-trained group of Space Pirate, designed to "hunt the Hunter," Samus Aran. They were equipped with improved conventional pirate weaponry, but also have powered energy shields, boostpacks, and a specially designed grenade launcher. Not to mention that they have armor that can even be compared to that of Samus'. Later on, Commandos would be retrofitted with Teleportation and Stealth Technology, among other minor upgrades. They often operate in pairs called "Commando Units". Even though they are very powerful, if a weapon can pierce through their Phazite helmets, it means certain doom for them. They are called at this time Commando Pirates.
It should be noted that there were two distinct forms of Pirate Commando Samus encountered in the Prime Series.
The first type of Commando was fought on Aether in Metroid Prime 2: Echoes. These Commandos were unique in appearance compared to the other Pirate Troopers, in that they were taller and wore distinctive enclosed helmets. They were well armed, carrying a grenade launcher with EMP grenades, a scythe for melee encounters, as well as a powerful shield which could deflect projectiles. The shield prevented the Pirates from utilizing their weapons while in use, however. They frequently used their jet dash systems to evade fire, whilst working in a team to bring down Samus.
A Squadron of Pirate Commandos entered Dark Aether on a reconnaissance mission from their base in the Agon Wastes. When Samus enters Dark Agon later on, she finds the entire Squadron deceased, due to a multitude of causes. These include exposure to the atmosphere of Dark Aether, explosion of Phazon canisters, attacks from the Ing Horde, and even friendly fire. Scans suggest that the friendly fire was due to panic in some cases, and in others shots to the top of the spinal cord as a punishment for cowardice, a common practice amongst Pirate Commandos. Later Samus discovers remains of two Pirate Commandos at the Phazon Grounds in the Sky Temple Grounds. They are being used as a food source for Dark Tallon Metroids. Scans reveal that one was taken by surprise by the Metroids, as indicated by his near-full ammo supply. The other "went out fighting" as his ammo supplies are empty.
The threat potential of Commandos, was elevated greatly when they were possessed by a Hunter Ing. As well as greatly increasing their damage ability and health, the Dark Pirate Commando gained a number of other devastating weapons. New abilities included the power to fire chunks of dark energy which could obstruct the visor, as well as to phase out of reality, thus becoming intangible. However, for some reason, a Dark Pirate Commando cannot use the shield or jet dash functions used originally. Despite these shortcomings, taking down a Dark Pirate Commando Unit makes for a difficult task. A Dark Beam Entangler shot can freeze them, allowing a Missile to shatter them instantly.
It should be noted, however, that when engaging Dark Pirate Commandos, should Samus take a long time in defeating them, the Commandos will phase away and the fight will end, rather mercifully.
Oddly, nearly every Pirate Commando Samus fought on Aether was Ing-possessed, making encounters with unpossessed Commandos a very rare fight in comparison. A massive horde of Commandos appears in Episode of Aether, invading a Federation vessel that Samus subsequently rescues. They are led by what seems to be a Commander, who wields enhanced Commando armor as well as a hand-held gatling gun.
The second type of Commando was encountered on the Pirate Homeworld in Metroid Prime 3: Corruption. These Commandos were distinctively different than those fought on Aether. They were similar in appearance to the other Pirate Troopers and had all of their weapons, but wore special armor crafted out of Phazite which could only be pierced by high-frequency beams. These tenacious warriors stood out against the lower ranked Pirates in their ability to become invisible, as well as their elevated endurance. However, one very easy way to kill a Commando Pirate was to combine the X-Ray Visor with the Nova Beam. The head of the Pirate could be clearly seen through their helmet, allowing a quick penetrating blast to destroy them.
The cloaking technology of these pirates may have been derived from that used by the Shadow Pirates, and is possibly located in their helmet, as they will not cloak themselves once the helmet has been shot off.
Whenever an alarm goes off, the following Pirates will soon be backed up by one or two Commandos, as they uncloak and sometimes roar in the area.
Pirate Commandos will sometimes enter Hypermode, which creates interference with Samus' X-Ray Visor. This makes it almost impossible to lock on to Pirate Commandos using the Visor and as a result makes it difficult to land Head Shots with the Nova Beam. However, Samus can lock on to a Commando using the Combat Visor, and switch to the X-Ray Visor (which keeps the lock-on while switching to the headshot view) and fire blindly at the head area in an attempt to do a Head Shot.
It is said that Pirate Commandos become Pirate Commanders if they withheld the rank for a minimal of ten years.