The wreckage of a disastrous Soviet space station, previously used for bizarre experiments on colossal arachnids, has crashed into New York City's intricate subway tunnels. The story follows Jason Cole, a steadfast subway supervisor, as chaos begins to unfold. Just as a warning siren blares and emergency teams scramble to evacuate the area due to fears of a catastrophic disease, Jason's coworker Jimmy ventures deep into the tunnels to investigate the source of the noise. He confidently reassures Jason, proclaiming, > "I think it's just the wreckage from that Russian spacecraft," but in an instant, he falls victim to a hidden menace, leading to a tragic electrocution when he tumbles onto the third rail.
At the site of the fallen space station, hazmat team members search for evidence of radioactive contamination amidst the debris. They recover a piece of wreckage, which is hastily delivered to a Russian doctor present at the scene who dismisses it as "nothing to worry about." Despite Rachel Cole voicing concerns over outstanding "waste disposal issues," the authorities declare the subway station safe for passengers just in time for rush hour.
A startling revelation ensues when a hospital pathologist uncovers strange "insect eggs" within Jimmy’s lifeless body. He hands Jason a canister containing these unsettling samples and instructs him to bring them to the health department for further analysis.
As the story shifts back to the subway systems, a foul stench prompts officials to halt operations once more. Pest control urgently removed an abandoned subway cart and stumbled upon the horrific sight of multiple deceased homeless individuals, cocooned within webs laden with eggs. One unfortunate soul is soon overwhelmed by a swarm of spiders, their grotesque movements making it seem as if they are macabre puppets.
In an effort to control the emerging crisis, authorities cordon off the area and reroute transit lines while misinforming the public about a supposed "virus outbreak." Meanwhile, a specialized team, equipped with protective gear, captures the marauding spiders and confines them within a vast enclosure. In the morgue, Dr. Darnoff collaborates with Russian investigators to conduct an autopsy on Jimmy, uncovering the presence of a queen spider egg symbiotically implanted within him.
Dr. Darnoff reveals that two decades earlier, a spacecraft buried in ice yielded alien genetic material which was injected into several species, but only spiders could endure these extraterrestrial genes. He emphasizes the queen spider's significance, capable of spinning limitless, lightweight protective material, which could provide military dominance to whoever controls it. In an unexpected turn of events, Colonel Jenkins dismisses Darnoff's cautions and orders the extermination of those who came in contact with the spiders, regardless of the doctor's warning that their eradication is unnecessary.
As a crisis unfolds, Rachel’s report reveals critical details regarding the eggs, leading officials to quarantine her apartment while trapping her sister Emily inside. In a desperate turn, Jason narrowly avoids capture and, upon examining the eggs, discovers an alarming lack of bacteria, an anomaly in nature. In a different location, operatives associated with Dr. Darnoff seize Rachel's purse containing the critical queen egg canister as she exits her underground garage.
As tension escalates, Rachel hurriedly contacts Jason, urging him to flee as they have unwittingly become targets of a merciless Russian scheme. Below the city, an unsettling transformation occurs as the spiders grow to terrifying sizes, emerging from the depths. Jason and Rachel rush to their apartment, determined to save Emily, who is trapped in a perilous situation. Venturing through the underground maze, they face colossal, toxic arachnids that attack without mercy. Yet, through sheer determination and clever tactics, they fend off these formidable creatures and reach the sanctuary of their apartment, only to find out through a frantic message that Emily has managed to escape and is hiding out at a nearby toy store.
As Jason's relentless quest to capture the queen spider intensifies, Dr. Darnoff intervenes, warning that seizing her could disrupt the fragile balance of their subterranean ecosystem. However, Jenkins, consumed by ambition, ignores this sage advice. Just as he is on the verge of capturing the queen, she erupts from the earth and devours the doctor, leaving Jenkins stunned by the unexpected turn of events.
Ultimately, Jason and Rachel find Emily in the toy store, but their joy quickly diminishes as they hear her desperate cries for help. Racing back into the tunnels, they encounter relentless hordes of spiders. Undaunted, they seek refuge behind a door and later find Emily, who is ensnared in sticky webs and desperately seeks her freedom.
They navigate back to the surface, aided by a precarious ladder as the queen pursues them relentlessly. In a brave act, Jason stomps on eggs lining the tunnel walls, enraging the queen and attracting her ire as she chases him. Utilizing a subway train, he maneuvers to lure her into a dead-end tunnel where her size proves her downfall.
With the queen trapped, Jason expertly steers the train backward through the narrow passage, but in the chaos, it collides with the queen, rupturing gas pipes and igniting a cataclysmic explosion that consumes the subterranean lair, including the monstrous queen.
As the inferno subsides, Jason, Rachel, and Emily reunite on the surface while soldiers work to collect the scorched remains of their arachnid foes. However, the eerie sight of a lone mutated spider crawling across a shattered traffic light hints at an ominous future as the screen fades to black.
