2009. Ten years of furious conflict and frenzied construction have turned an alien wreck into a human triumph: the colossal space battleship Macross. On the day of the ship's launch, the world waits with bated breath to witness mankind's next giant leap. Hovering above the planet, though, the Zentradi, a merciless warrior race, seek to advance its agenda of destruction and conquest...

Locked in mortal combat with the attacking Zentradi fleets, the Macross has finally fought its way across the solar system to Mars, where an abandoned base may offer temporary safe haven. But this planet is named after the god of war and the hoped-for sanctuary proves to be a deadly trap. With the lives of 56,000 human survivors hanging in the balance, Misa Hayase must put her own life on the line in a desperate gamble that will most likely cost her everything.

A dangerous escape leads to an unpleasant homecoming as the crew of the Macross find themselves pawns in a much bigger game. Not only are Earth's forces badly divided, but now the Zentradi have defied the rules of science to place spies on board the Macross itself!

Betrayed by the military of their own planet, the crew of the Macross find themselves trapped on the Earth, unable to evacuate their civilian passengers even as the Zentradi attacks continue to rain down from the skies. In the air, a new rivalry begins as enemy ace pilot Millia finds her ultimate opponent in the person of Max Jenius, while on the ground Misa is consumed by guilt after an accident that sends a critically wounded Hikaru to the infirmary.

Strange things are happening within the Zentradi fleet: secret meetings, use of contraband materials and even hints of civil disobedience from previously unshakable warriors! The female Meltran fleet is affected as well, as one of their finest abruptly goes rogue on a path of personal vengeance.

The Macross is now allied with the same Zentradi fleets they have fought for over a year, but even an armada of a thousand ships is nothing against the overwhelming juggernaut of over four million ships that now oppose them. But Mankind has a secret weapon that has thus far repelled every attack against it. Can the force the ancients called "Protoculture" save the Earth from total destruction once again?

The battle for the Earth over, but the battle for the future has yet to be fought. As rogue Zentradi continue to mass in the desert wastelands, the allied human and giant forces in the cities find themselves driven back to the edge of war. Mankind's last hope: the rebirth of the Macross.