The pirate capital ship is a type of warship used by the Kel-Morian Combine. It can be equipped with an electric field generator or a cloaking device.
It is called a "Cerberus" In the galaxy map editor. There is also a doodad of a normal ship and adocked ship used in some multiplayer maps called a "Cerberus construction dock".
Game Unit
A pirate capital ship can be found in the Heart of the Swarm mission "With Friends Like These...". The player can choose to engage it with the Hyperion. The pirate ship can disable the Hyperion with its electric field generator, but once destroyed, the Hyperion can use the generator itself.
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References
Blizzard Entertainment. StarCraft II: Heart of the Swarm. (Activision Blizzard). PC. Mission: Heart of the Swarm, With Friends Like These... (in English). 2013-03-12.