The Pirate Warship (also known as a Space Pirate heavy-assault ship) is a spacecraft belonging to Space Pirates and boss in Metroid Prime: Federation Force. In M16: Slipstream, the Federation Force is tasked with going to Bion to reactivate a communication tower on an ancient skiff, but they come under fire from this warship, forcing them to destroy it. The soldiers utilize catapults which fire boulders at the ship to damage it. The boulders must be pushed into into the catapults using weapons fire, much like in Blast Ball. The warship will summon Dropships to defend itself, and launch bombardments of three purple projectiles at regular intervals. These projectiles rather resemble the spheres fired by the Berserker Lord, although unlike the Berserker's projectiles, the Warship's cannot be fired back at it. They can however be destroyed. The projectiles will impact the skiff and create holes. While this will not cause immediate problems with maintaining flight, the holes may cause the Force to forfeit the bonus objective of not losing any spheres. Destroying the projectiles before they impact will prevent this.

Soldiers need to hit the Pirate Warship 8 times within 10 minutes until it explodes; otherwise, the mission fails.