On an unnamed planet inhabited by the Arachnids, a squad of soldiers find themselves pinned down and surrounded on all sides by Arachnid forces. Even with their new laser gun technology and assistance from psychic soldiers, the Arachnid assault overwhelms them and General Jack Shepherd (Ed Lauter) decides to make a last stand with several of his best soldiers, allowing the majority of his surviving troops to escape. The plan works, and the soldiers, whom include Sergeant Dede Rake (Brenda Strong), the psychic Lieutenant Pavlov Dill (Lawrence Monoson), Private Jill Sandee (Sandrine Holt) and her lover Private Duff Horton (Jason-Shane Scott), and Private Lei Sahara (Colleen Porch) escape. Despite reaching relative safety, the team is whittled down by deadly dust storms and Arachnid ambushes. Among these deaths is the only member of the platoon with a radio, Corporal Thom Kobe (Brian Tee). Lieutenant Dill finds himself unable to command his soldiers as he receives traumatic visions of utter annihilation. He takes his anger out on Private Sahara, who is revealed to have been psychic but lost reliable control of her psychic abilities as puberty took place, which seems to be rather typical. The remaining refugees find themselves sheltering within Hotel Delta 1-8-5, an old and abandoned structure containing Captain V.
J. Dax (Richard Burgi), a disgraced (though with a fantastic combat record) soldier who had killed his commanding officer and was sealed in a furnace-like cell to be taken back to Earth to be court-martialled for his crime. As a deadly dust storm kicks up, the soldiers find themselves without communications or back-up for a lengthy period of time and protect themselves through the use of electric pulse fences with limited battery power to hold off the Arachnid warrior bugs. Dax takes command of the small group, much to the annoyance of Dill, and the two develop an instant dislike to each other at first sight. Dax sees Dill as an incompetent commander, while Dill sees Dax as a traitor to the Federation. Soon after defenses for Hotel Delta are set up, Shepherd and three of the soldiers return.
While the troops in the outpost originally think that all of their comrades has reached safety, it becomes clear that, in fact, all their comrades died. But Shepherd was rescued by three of his fellow soldiers. In addition to Shepherd, the three troops include the near-catatonic Private Charlie Soda (Kelly Carlson), the odd acting Tech Sergeant Ari Peck (J. P. Manoux), and the medic Private Joe Griff (Ed Quinn). With the help of the newcomers, they solve all of their technical issues, including lack of communication. After General Shepherd manages to radio to the Starfleet, they now need only to wait for a Fleet dropship to rescue them, but it may take several hours due to the fleet being on the other side of the planet. Tempers flare at the base as Soda seduces both Horton and Sandee.
In a rage, Soda finds a new significant other in Griff. However, both Horton and Sandee soon act strange, as do many other survivors. Sahara seems to have become ill as she has nightmares and wakes up vomiting. Accidentally brushing Griff's hands brings on a psychic vision in Sahara. Sahara goes to Rake for advice and tells her what really went on.
Rake suggests that Sahara is simply pregnant and that pregnancy not only brings on the symptoms she describes, but makes girls temperamental and makes them think that "they know it all". Eventually, Sahara and Dax find themselves facing a new breed of Arachnid, a small bug that infests the human body by forcing open the mouth and propagating inside the brain. They come to Dill with their news and make amends with him, also learning that he only made bad decisions because of the visions he was receiving and that he felt incredibly guilty over the loss of men under his command in the escape. Sahara tells Dill that she has been receiving parts of the vision as well, and Dill reveals to Sahara that an occasional side-effect of pregnancy is the temporary return of the psychic abilities lost at puberty. Soon after making amends, Dill corners several infected soldiers and intends for them to be captured and studied, but as he insults them another infected soldier kills him with a knife that Dax gave him earlier. The assault is blamed on Dax (his name was inscribed on the knife) and he is imprisoned again in the cell.
Eventually a dropship finally arrives but all of the troopers are infected including Shepherd, who, if returned to Earth, may infect the leaders of the Federation. Rake takes multiple adrenaline shots, wounding one infected soldier and killing another before freeing Dax, but kills herself because she has also been infected (Note: it is unclear why the parasite was unable to control her, perhaps because of the adrenaline shots). A soldier attempts to infect Sahara, but after several unsuccessful attempts to stop him, Sahara manages to kill him and escape. Sahara uses her restored psychic abilities to read the mind of the bug that had attempted to control Rake's mind and discovers the bugs plan: use General Sheppard to infest High Command allowing the bugs to wipe out the human race on Earth and cause Sahara's vision to come true.
Sahara and Dax kill the rest of the infected troops, and make it to the roof of the structure to confront the infected Shepherd just as the pulse fences give way, allowing thousands of warrior bugs to swarm over Hotel Delta. Just as Shepherd is about to be rescued, Dax kills him with two rifles held akimbo. He gets Sahara onto the ship and tells the bewildered crew that she holds information vital to the survival of the Federation. He then refuses to get onto the ship ("Murderers don't go home!") and vows to give her time to escape.
Dax goes down in a blaze of glory, fending off bugs as they overwhelm him. Planet Earth, one year later. Although Dax is labeled as a Hero of the Federation, his death is shrouded in propaganda as the Federation uses his end as a means of recruitment. Sahara and her newborn baby attend a lecture by a recruiting officer whom is encouraging visitors to join up in the continuing war against the bugs.
Having received an honorable discharge from the military to raise her infant son, Sahara walks out of the recruiting station. The recruiting officer walks up to Sahara after the lecture and thanks her for attending, and then, after seeing her baby that she is holding, urges her to raise her son well for: "we need fresh meat for the grinder". Sahara, alarmed, flees the recruiting station. This act appears to have no effect on the recruiter, showing the movie's take on military idealism..