However, Cold War tensions between the United States and the Soviet Union have not ended; rather, they have escalated as both sides continue to militarize space, and the shadow of nuclear conflict looms over humanity both on and off Earth.

The UN base is captured in the crossfire and quickly destroyed, eliminating all but six members of the "Cosmic Culture Club"—Elizabeth, Arthur, Roan, David, Simone, and Anna, leaving them stranded on the barren planet that has suddenly become a battlefield.

As the battle ends, the lone SPT standing lands next to the terrified group and opens up revealing a pilot, who simply announces to them, "The Earth has been targeted".

The robots who destroyed the UN base were the creation of the Grados, an alien race, from the Udoria system, who came to the Sol system for conquest, seeing an easy victory as the two superpowers raged against each other to exhaustion—however, this could also be described as an act of pre-emptive self-defense; the Gradosian supercomputers have determined that humanity will eventually cease its in-fighting and become powerful enough to spread through the galaxy, feigning a deadly threat to even the far off Grados.

The first ED song, which was for episodes 1-25, was Go-fun Dake no Wagamama (Just 5 Minutes of Selfishness), also composed by Hideya Nakazaki and performed by Seiko Tomizawa & Airmail from Nagasaki.

For example, Eiji's first appearance is just after the resolution of Martian Successor Nadesico, and the SDF-1 Macross's fold removes the heroes from Earth long enough for Grados to establish control over Manhattan.

The heroes return in time to aid the resistance, and Eiji finally joins the team officially along with Domon Kasshu after they (and the player's current character) fight off the Demon Death Platoon and several Gundam Heads.