On an asteroid, the Terran Federation’s Fort Casey is crawling with bugs. The starship Alesia begins to deploy its Mobile Infantry troopers, by dropship, to seize and control the hangar and rescue any survivors. Lieutenant Daugherty’s ‘Alpha’ team lands and immediately engages bugs, fighting through to rendezvous with the surviving Fort Casey troopers. After setting explosives charges, the troopers head to the starship John A. Warden for evacuation, only to see it leave dock without them – Minister Carl Jenkins has commandeered the Warden from Captain Carmen Ibanez, sending her to Alesia. Before leaving, Jenkins orders that Major Henry “Hero” Varro, the commander of Fort Casey’s K-12 troopers, be escorted to Alesia as a prisoner. Alesia docks with Fort Casey for emergency evacuation of the surviving troopers, and the Fort Casey asteroid is successfully destroyed.
While en route to Earth, Alesia is contacted by General Johnny Rico from High Command at L-6 Base. When he orders Alesia to search for the Warden, which has broken all contact, the Fort Casey troopers agree to do so on condition that Varro leads them during the mission. When they find the Warden, Daugherty’s team escorts Ibanez to the bridge while Varro’s team secures the Engine Room, both teams finding nothing but dead crewmen and a few dead bugs. Varro finds a deranged Jenkins and is warned – too late – not to power up the Warden as ‘she’ has hacked all the systems. As the engines recharge the Warden, an Arachnid Queen inside takes control of all systems and opens bulkhead doors to release her bugs. As Ibanez and the troopers attempt to return to Alesia, the Queen uses the Warden’s main weapons to destroy the other ship, then flies Warden into a wormhole whose outlet is in near-Earth space. The troopers return to the Warden’s bridge, where Varro reveals he was arrested when Jenkins had ordered his unit to capture the Queen alive on Fort Casey, but Varro had refused to sacrifice his squad.
General Rico deploys three starships from the L-6 Base in Earth orbit, but they are unable to stop the Warden. The Queen sets the bug-infested Warden on a trajectory to crash land in Paris, but Alpha Team sniper Trig manages to shoot out the wires linking the Queen to the ship, allowing Ibanez to re-direct the Warden to crash in a mountain range. Meanwhile, General Rico leads a squad of troopers in Marauder suits to stop the bugs from escaping the crash site, while high command gives him 30 minutes before they will drop nukes from the L-6 Station to sanitize the site.
Back on the Warden, the five surviving troopers make their way towards the Queen. Ice Blonde protects Ibanez at a nearby airlock while Mech and Ratzass go to the engine room to blow it up. When Varro and Bugspray find Trig’s corpse, Bugspray uses Trig’s family-made sniper rifle to buy Varro some time to reach the Queen. Jenkins, having recovered from his mental breakdown, provides Varro back-up with bugs under his mind control – revealing an important Terran breakthrough in the war and the reason for capturing a live Queen.
Rico is the only one from his squad to reach the Warden. The extraction shuttle from L-6, and the nuclear strike, are all destroyed by the Queen’s control of the Warden’s weapons. As Jenkins leads the team to his shuttle from Fort Casey, Rico rushes to distract the queen and rescue Varro. Varro, critically injured, blows a grenade when surrounded by bugs. Rico abandons his broken Marauder suit and uses a combat knife on one of the Queen’s eyes, buying Ibanez time to make take-off preparations. Rico barely sprints back into the dropship as it escapes the Warden before the explosives detonate and destroy the Warden.
Mech, Ice and Ratzass pay their respect to their fallen comrades while Ibanez confronts Jenkins over the recent crises. Jenkins sidesteps the issue, telling Rico and Ibanez that his research will someday save the entire galaxy. In the aftermath, one warrior bug is seen navigating a sewer system, having survived the Warden’s destruction.