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An unknown airborne outbreak devastates the United States as the Air Force bombs the town. Ray, Claire, and their daughter Zoe seek refuge in an abandoned fallout shelter, hoping to wait out the chaos. They begin a tense new routine focused on safety and survival.

Zoe wakes from a nightmare about the Breathers, heightening the fear in the cramped shelter. The family agrees on a set of rules—stay calm, stay hidden, and do whatever it takes to protect Zoe. The shelter becomes a fragile sanctuary against a deadly, unseen threat.

Rations are dwindling and a rat starts feeding on their supplies. The family resolves to kill the intruder and protect what little food remains. During the effort, they discover a small air duct near the barricaded hatch that could offer a route to safety without breaking the rules.

Claire kills the rat, but Ray accidentally knocks over a lamp, starting a small fire on a wooden table. The smoke begins drifting up the air duct, slowly giving away their position to any Breathers nearby. Ash on the hatch makes their hiding place visible to outsiders.

Ray and Claire go to the surface to cover the shelter entrance while Zoe uses a homemade periscope to peek outside and spot a distant humanoid. Ignoring the rules, Zoe climbs through the barricade to warn her parents. The family quickly retreats inside as the Breather closes in.

The Breathers continue their approach and the family tries to stay quiet, but Zoe's doll Olive becomes snagged on a pipe screw and activates, drawing unwanted attention. The Breather breaches the shelter in their search, and danger escalates.

In a flashback, the family rides a highway fleeing Kingsville, only to be stopped by the CDC who place signs declaring a quarantine. The memory reveals how quickly the world collapsed and their proximity to the outset of the outbreak. The panic and isolation of the quarantine frame their past and present.

In the present, additional Breathers reach and breach the shelter hatch. Claire and Zoe escape through the air duct, but Ray is captured and disappears amid a spray of blood. The family is separated and their chances of staying alive become even more precarious.

In another flashback, military jets bomb the town while the family hurries toward a nearby shelter. Claire injures herself and discovers that the virus is airborne; the discoloration of her blood confirms infection and explains the spread of the outbreak.

Back in the present, soldiers test Claire and Zoe's blood and question them to locate other survivors. Ray suddenly appears, kills a soldier, and demonstrates surprising strength as more soldiers open fire and he is nearly killed.

Ray is shot repeatedly and dies after a brutal rampage. Claire and Zoe witness a fierce transformation in Claire as she channels Ray's power. Zoe, enraged, tries to attack Claire but is restrained by Claire's remembered rule to stay calm.

Claire and Zoe manage to escape the net and flee as the helicopter arrives, while Ray's body remains behind. They head toward a nearby sewer system to hide and survive, away from the soldiers outside.

In the sewer, they encounter Joey, Zoe's friend and neighbor who has also survived. He guides them to other unknown survivors living beneath the city, suggesting there is a community of infected or sheltered people underground.

Zoe notes that they have survived to 'day 302' as the sun rises through a nearby window. Claire counters that these are miracles, not days, echoing the language Ray used at the film's start. A quiet moment passes as they absorb the grim truth of their new world.

Claire looks up toward the light through a sewer opening and then climbs through, joining the group of survivors waiting below. Zoe follows, and they prepare to live among the underground community of others who have endured the outbreak.