Phantom Boss

The Phantom is the elite version of the Black Prince boss. It appears similar to the Black Prince, but has a crow's nest on the main mast. In addition to the Black Prince's normal abilities, the Phantom has modified barrels that, on impact with the player/water, leaves behind a toxic patch in the water. The Phantom also sends smaller ships to suicide ram the player. The smaller suicide boats, Ship of the Dead, cause a Debuff effect to the player upon impact, much like an Engineer's pulse ball. This is the rarest enemy in the game.
Ship of the dead

Ship of the Dead, in comparative scale with a Battlecruiser

Fortress Destroyer Enemies
Ships Skimmer (Speeder) · Raider (Pirate) · Ranger (Hunter) · Engineer (Senior Engineer) · Brimstone (Purifier) · Basher (Crasher) · Zealot (Fanatic) · Skirmisher ·
Aircraft Viper (Asp) · Locust (Harbringer) · Hydra (Drake) · Raven ·
Towers Cannon Tower (Barrage Tower) · Cannon Battery · Sea Cannon (Blaster Tower) · Missile Tower (Onslaught Tower) · Missile Battery · Sea Missile (Splinter Tower) · Onslaught Battery · Bridge Tower · Barrage Battery · Missile Cluster ·
Bosses Herald · Vanguard (Bloodguard) · Hive (Brood) · Leviathan · Nexus (Median) · Kraken (Kraken v2) · Black Prince (Phantom) ·
Other Plasticyte · Ship of the Dead · Broken Tower · Metal Gate
Buildings Shipyard · Air Base · Shield Generator · Storage Yard

Enemies listed in parentheses () following another enemy are the elite form of that enemy. If there is no elite form listed, that means one does not exist or has not yet been added to the game.