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Cloaked Troopers are Pirate Troopers employing cloaking technology. They are encountered in Metroid Prime: Federation Force. Cloaked Troopers are somewhat similar to Shadow Pirates, although their cloaking technology has advanced since the Pirates' Glacier One operations. Cloaked Troopers are encountered in later missions in the game, such as M13: Phantom. Cloaked Troopers tend to act as a type of stealth assassin, using their cloaking technology to move in on enemies undetected and engaging them in melee combat using blades rather than ranged weaponry.
During the first mission in which cloaked troopers are encountered information can be found on a pirate log that indicates that the cloaking technology they use was developed at this facility on Talvania.