Shadow Pirates use cloaking technology, and so are difficult to spot with the Combat Visor. They first appear in the Space Pirate Research Lab in Phendrana Drifts after Samus collects the Thermal Visor. They replace the standard Space Pirate troopers that initially guarded the base and will attack in the darkened lab and foggy areas. Since Shadow Pirates do not have ranged weapons, they are only dangerous in close quarters.
Note that Shadow Pirates specialize in ambush attacks and will pop out of vents for quick, lethal strikes. Be especially cautious in the narrow corridors of the Space Pirate facilities in the Phazon Mines.
Dash with B to dodge their attacks and circle around them. In close quarters, use Missiles to quickly defeat them or use the Ice Beam and a single Missile to shatter them.