The Heavy Missile was an anti capital ship weapon commonly used by the Vaygr in Homeworld 2. It was a large missile armed with a high yield warhead, possibly a small nuclear fusion device. In terms of raw firepower, it rivalled the Hiigaran Ion Cannon technology, but was arguably more versatile. The self-propelled homing missiles did not require the ship they were launched from to track the target with its guns, and thus allowed for evasive maneuvers and repositioning while maintaining fire.

Heavy Missiles were used on the Heavy Missile Platform, the Heavy Missile Frigate, the Destroyer, and the Battlecruiser

Like the Hiigaran ion cannons, it is also believed that the heavy missile was available in varying classes. The light version of the weapon was used in the Heavy Missile Platform, and dealt less damage per missile than the medium variant equipped by the Heavy Missile Frigate. The Vaygr Destroyer either carried similar missiles to the Heavy Missile Frigate's or a heavier class. Lastly, the Vaygr Battlecruiser utilized the heaviest class of missile, a single salvo of 8 missiles able to damage the hull of a Battlecruiser considerably.