As the REF prepared for the Battle of Reflex Point, the SDF-3 and the science vessel Deukalion conducted a test of the Neutron-S missile on an uninhabited planet in the Omicron sector. Not realising the devastating potential of the weapon both ships were badly damaged during the detonation of the weapon, which created a Black hole.
While attempting to fold away from the black hole the SDF-3 was rammed by a Haydonite ship, preventing it from folding with the Icarus, which had been dispatched to reestablish contact with the SDF-3, and send it towards the black hole.
The fate of the SDF-3 was unknown, by either side. The Haydonites had believed that the SDF-3 had fled by to Space Station Liberty and were surprised to find it not there when they attacked. Following the loss of Liberty the REF dispatched the Ark Angel to search for the missing vessel and its critically important Protoculture Matrix. (Robotech: The Shadow Chronicles)