These incredibly powerful missiles were originally created by the Karbarrans for use against the Robotech Master's home planet, but they couldn't bring themselves to use them, and they were placed in storage. After the Sentinels defeated the Regent's forces, the REF found out that the Regis had captured Earth. Concerned that they would be unable to fight yet another powerful Invid force, the REF purchased several Neutron-S missiles for use as a last-ditch effort, with the intention of destroying all life on Earth, including the Invid.
Upon the defolding of the SDF-3's fleet in Earthspace, the missiles were fired. The Regis, sensing thier power, purposely directed her pheonix of mind-stuff to fly through them (and the REF fleet), destroying all it touched, thereby sparing Earth from the fate of her home planet, Optera.