Having been rescued from the fallout shelters of whatever is left of Macross Island, the citizens attempt to normalize their life aboard the giant battle fortress. Roy Fokker encourages Rick to join the Robotech Defense Force. The SDF-1 crew discover that the spacefold drive they used to make the jump has disappeared, but stumble upon an idea to transform the ship. The idea is soon tested in a battle with the Zentraedi, but renders much damage to Macross City.

The SDF-1, transformed back into ship mode once more, arrives at a human outpost on Mars to gather fresh supplies, but discover that the base was damaged in a battle years before and had no survivors. However, the Zentraedi lie in wait with a new commander, Khyron, raring for glory by using gravity mines to trap the ship. In the midst of the fight, SDF-1 First Officer Lisa Hayes tries to find out whether her old fiance, Carl Riber, is still alive.