In 2199, after five years of attacks by an alien race known as Gamilas, the Earth Defense Force launches a counter-offensive near Mars. The fleet's weapons are no match for the Gamilas, who easily wipe out much of the force. During the battle, EDF captain Alex Wildstar volunteers to use his damaged ship, the destroyer Paladin, as a shield to cover Captain Abraham Avatar's ship, allowing his escape. Alex's ship is destroyed.
On Earth, Alex's brother Derek is scavenging on the irradiated surface near the half-buried wreck of a WWII battleship, when an object impacts near him & knocks him unconscious. He awakens to find an alien message capsule. Derek also notices that the radiation has been reduced to safe levels around him. He is rescued by Avatar's returning ship & it is discovered that the capsule contains engineering schematics for a new warp drive & coordinates for the planet from which it came (Iskandar). After learning what happened at Mars, Derek accuses Avatar of using his brother as a sacrificial lamb & tries to hit him, but crewmember Nova Forrester violently stops him.
Avatar believes the hope for humanity lies within Iskandar. A request for volunteers for the mission is sent out, & Wildstar - a former EDF pilot - decides to re-enlist. Their last battleship, the long-dead Argo, is rebuilt & enhanced with alien technology. Before the Argo can launch, the Gamilas attack with a gigantic missile. Captain Avatar gives the order to fire the yet-untested Wave Motion Cannon, which successfully destroys the incoming missile. Wildstar is reunited with his old fighter squad. Nova, who joined the EDF years ago because of her admiration for Wildstar, is bitter towards him.
The Argo crew performs their first warp test & encounters more Gamilas ships. Since the Wave Motion Cannon is powered by the same reactor as the warp drive, the crew has to wait until the engine recharges before they can warp again. The Argo destroys the alien capital ships, but the battle damages Nova's fighter. Wildstar launches to rescue her & is sent to the brig for disobeying orders. Venture, Wildstar's former squad-mate, tells Nova that Wildstar left the service because he accidentally caused the death of his own parents & also Venture's wife during a mission.
After warping out of the Milky Way, the Argo crew finds a Gamilas fighter adrift & recovers it to study, but the alien pilot is still alive & possesses Commando Team Leader Webb Knox, in order to communicate. The alien calls himself Desslok & says the Gamilas are a race with a hive mind. Wildstar stuns the possessed Knox, but the alien apparently is destroyed.
Later, an ailing Captain Avatar makes Wildstar the acting-captain. The crew discovers the captured Gamilas fighter contains a homing beacon, giving away their position. The Argo fires its Wave Motion Cannon to destroy a Gamilas ship, but a stealth Gamilas spacecraft latches onto the ship's occupied third bridge on the bottom of the hull. Wildstar reluctantly orders Nova, in her fighter, to blast the third bridge support away moments before it detonates, saving the Argo but killing several crew. Wildstar apologizes to Nova for ordering her to doom their crew-mates, & they have an intimate moment as the ship warps again.
The Argo arrives at Iskandar, but is met by a large Gamilas fleet that sends a spacecraft to obstruct the muzzle of the Wave Motion Cannon. With their main weapon disabled, Wildstar makes the dangerous choice to conduct a random warp & ends up at the opposite side of Iskandar. They are surprised to see that it is lifeless, & in fact strongly resembles Earth in its presently irradiated state. It is then discovered that Gamilas & Iskandar are the same planet. The crew thinks it is a trap, but Wildstar urges them to go ahead. He leads an attack party to the planet's surface against heavy Gamilas opposition. Much of the assault force is killed, & the remaining pilots stay behind to cover for Wildstar, Sandor, Knox, & Forrester as they head for the coordinates.
Once they reach the coordinates, an alien possesses Nova's body & explains that the Gamilas & Iskandar are two aspects of the same race. The alien says their planet is dying & they saw Earth as the most suitable replacement, after first killing off humanity. Iskandar did not agree with this & was imprisoned. Iskandar implants in Nova the ability to clean the radiation from Earth. As she & Wildstar return to the Argo, Knox & Sandor sacrifice themselves by destroying the Gamilas power source. The Argo returns to Earth, where Avatar dies. The crew rejoices at their return home, but a surviving Gamilas ship ambushes them & severely damages the warship. Desslok now appears & says they no longer wish to invade the Earth; however, since the majority of the Gamilas were killed, he intends to destroy the planet with his ship to avenge his race. Wildstar orders the surviving crew to abandon ship before he pilots the Argo on a suicide attack against Desslok's ship. He fires the blocked Wave Motion Cannon, which destroys both spaceships.
The ending shows Nova standing with a child, implied to be Wildstar's son, on the Earth's surface now restored to its original state.
- Derek Wildstar
- Nova Forrester, Black Tiger Squadron ace pilot
- Stephen Sandor, chief science/technology Officer
- Mark Venture, chief navigator
- Dr. Sane, ship doctor
- Chief Orion, chief engineer
- Sergeant Webb Knox, Space Commandos leader
- Homer Glitchman, communications officer
- Dash, tactical unit
- Peter 'Pete' Conroy, Black Tiger Squadron commander
- Jefferson Davis Hardy, Black Tiger Squadron member
- Captain Abraham Avatar
- Christopher Eager, navigator
- Alex Wildstar, Derek's older brother & captain of the space destroyer Paladin