The Negative Energy bomb is a powerful weapon, with similar capabilities to a Nova bomb. It is a large missile that is on Glorious Heritage Class starships and is housed inside a silo on deck 12. The targeting systems are quite primitive under manual control, as Harper puts it as "looking through a periscope", with the AI control being better in the targeting systems to fire the missile. The Missile is capable of destroying a Magog Satellite Ship and may even be able to destroy the Magog World Ship. However, a Glorious Heritage Class has very few Negative Energy bombs, and there is not really a need to use it, exept in dire situations. It is classified as a "strategic weapon" which makes using it in most situations out of the question. ("Symmetry of Imperfection")
It is known that the Negative Energy Bomb was used once by the Andromeda Ascendant to eliminate a Magog Satellite Ship.