In the late 22nd century, planet Earth has come under attack by an alien race known as the Gamilons. The resulting war has favored the Gamilons, whose bombardment of the Earth has left the surface without any life and Earth's surface too contaminated for human survival, so the survivors have migrated underground. Now, however, a new threat has emerged -- the radioactive contamination on the surface has begun to work its way down into the Earth. In less than a year, all life on Earth will die. Meanwhile, Earth's remaining space forces continue to fight against the Gamilons, but the Earth fleet has been reduced to one operational space battleship (commanded by Captain Avatar) and a few supporting missile ships, including the Paladin (commanded by Alex Wildstar). This task force engages a Gamilon fleet near Pluto, but the Gamilons outnumber the Earth fleet five-to-one, and soon decimate the Earth ships. The Paladin and the other support ships are destroyed while covering the retreat of Avatar's flagship.
During the battle, an unidentified space vessel enters the Solar System and is damaged in the cross-fire. It crash-lands on Mars, where it is investigated by cadets Derek Wildstar and Mark Venture. They discover a beautiful, dead alien woman, ejected from the escape pod, clutching a message capsule. Shortly thereafter, retreating from the Pluto battle, Avatar's crippled battleship retreats to Mars, where Derek Wildstar and Mark Venture board to hitch a ride back to Earth. Once aboard the battleship, Derek Wildstar makes the observation that his older brother, Alex, did not survive the Pluto battle. The battleship returns to Earth and arrives at an underground city where the crew leaves on liberty. The message capsule is analyzed and the message decoded. It has been sent by Queen Starsha, of planet Iscandar, who offers Earth the Cosmo DNA, a device which can remove the radioactivity. The woman who carried the capsule was Starsha's sister, Astra. The message also contains plans for an advanced-technology Wave Motion Engine -- capable of faster-than-light travel. Even with this advantage, is it possible to make the journey in time?
As the Earth Defence Command deliberates, a Gamilon recon plane is detected sniffing around the ruins of the sunken WWII battleship, the Yamato. Out of sheer boredom, Wildstar and Venture take a plane out (unauthorised) to investigate. They lose the Gamilon, but discover the hulk of the Yamato, only to be left wondering why Gamilon would be interested in it. Could there be some secret?