The Kiowa gunship helicopter carrying the Delta Force team, led by Delta-One, heads toward Rachel’s location. The team pinpointed her position by gaining access to the reception frequencies of Pickering’s cell phone and tracing the coordinates of Rachel’s incoming call to him. 

To approach their target, the Goya, without being detected, Delta-One flies a deceptive course, appearing as a small cargo plane on the ship’s radar. Once close, the team activates an “umbrella” radar-jamming system, which blankets the Goya in electronic noise, disabling all its radar and communication systems. The Delta Force team prepares to attack the isolated and defenseless ship. Meanwhile, at the White House, President Herney is awakened at 3:17 am by an emergency call from Ekstrom.

Aboard the Goya, Tolland shows Rachel a marine-biology database called Project Diversitas—which he jokingly nicknames “LOBSTER”—to search for organisms similar to the meteorite fossil. Limiting the search to deep-sea trench habitats, they discover Bathynomous giganteus, a large, louse-like isopod that closely resembles the fossil. 

Tolland theorizes that the meteorite is actually a piece of Earth’s crust containing the fossilized creature that was then subjected to chondrule-forming pressure in an oceanic trench. He notes that the resemblance could be used to support NASA’s panspermia theory unless the meteorite’s authenticity is questioned. Just then, Xavia and Corky announce that their microprobe analysis shows that the rock has a titanium/zirconium ratio consistent with Earth rock, confirming that it’s a fraud. As Rachel gathers the evidence, Tolland discovers that the ship’s phones are dead. The Coast Guard pilot then runs in, announcing that all radar and communications have failed.

Inside Sexton’s office, Gabrielle tries to access his computer. She initially types “SSS,” the password she guessed a week prior, but it fails. He has changed it.

A gunship helicopter attacks the Goya, strafing the deck with bullets and grazing Rachel’s arm. As everyone scrambles for the Coast Guard helicopter on deck, the attackers use a laser to target it. Rachel tackles Corky and Tolland to the deck just as a Hellfire missile destroys the helicopter, killing the pilot and Xavia. The explosion sends flaming debris across the ship. Tolland pulls a stunned Rachel to her feet as the wreckage sinks into the sea.

Ekstrom confesses to Herney over a videophone that NASA faked the PODS discovery. He explains that NASA intercepted a radio transmission from a Canadian who found the meteorite but then died in a storm. With the meteorite’s coordinates and PODS orbiting nearby, Ekstrom decided to claim it as a NASA victory to counter Sexton’s attacks and boost the president’s failing polls. Herney is furious, realizing that the deception undermines his entire presidency. Meanwhile, Sexton paces his apartment, impatiently waiting for Gabrielle.

After failing to crack Sexton’s password, Gabrielle is about to leave when she notices “POTUS” (president of the United States) written in glitter on his desk calendar. She tries “POTUS” as the password, but it also fails. Defeated, she starts to leave through the bathroom when her phone rings. It’s Sexton, asking where she is. Gabrielle lies, claiming to be at her office, but Sexton sounds suspicious. After hanging up, Gabrielle doesn’t realize that Sexton could hear the distinctive triple-tick of his prized Jourdain grandfather clock audible nearby.

Tolland, Rachel, and Corky flee belowdecks to escape the helicopter attack. They descend to a grated catwalk hanging over the ocean, where Rachel is terrified by the sight of hammerhead sharks circling below. They head toward a small powerboat moored in an underwater dive area. As Corky unties the boat, the helicopter appears and opens fire, wounding his leg. Corky gets the boat started just as the helicopter targets it with a missile. Tolland fires a flare gun at the helicopter, causing the pilot to veer and the missile to miss, instead striking the base of the strut 30 feet beneath Rachel and Tolland. The explosion damages the ship and destroys the stairs, trapping Rachel and Tolland on the catwalk.

Corky speeds away in the powerboat, hoping to draw the helicopter away in a “divide and conquer” strategy. He watches in horror as the chopper instead lands on the Goya, deploys two soldiers (Delta-Two and Delta-Three), and then takes off in pursuit of him. Belowdecks on the Goya, Delta-Three descends to find Rachel and Tolland. As Delta-Three prepares to shoot Rachel, Tolland ambushes him from below, using a “bang-stick”—a pole tipped with a shotgun shell—to blow off the soldier’s foot. Tolland orders the captured Delta-Three to tell the helicopter to back off, but the soldier looks directly at Tolland and deliberately tells the pilot to destroy the departing vessel instead.

As Gabrielle prepares to climb out of Senator Sexton’s private bathroom, she notices his “SS” monogrammed cufflinks. The sight of the initials, combined with the “POTUS” on his calendar and the slogan on his screensaver, gives her a new idea for a password. She returns to his computer and successfully logs in with “POTUSSS.”

As the Kiowa helicopter pursues him, Corky discovers that the powerboat’s radio has been destroyed by bullets. He realizes that the ocean current has caused the boat to travel in a large circle, bringing him back toward the Goya. To mask the scent of his bleeding leg from sharks, he urinates on the wound and on a rag he uses to wipe himself down. As the helicopter targets him with a laser, he puts on a life vest. He’s standing at the rear of the boat when the missile hits. Aboard the Goya, Tolland hears the explosion.

At the White House, Herney’s aides inform him that they can’t locate Tench. They believe that she may have gone to meet with Pickering, who is also unreachable. A Secret Service agent then enters and reports that there was a car bombing at the FDR Memorial and that the victim has been identified.

The captured soldier, Delta-Three, awakens bound and gagged on the Goya’s main deck. His partner, Delta-Two, follows a blood trail and finds him. As Delta-Two approaches, Tolland, hidden inside the Goya’s attached Triton submersible, uses its robotic claws to trap him. Delta-Two fires his machine gun at the sub, but the bullets fail to penetrate its thick acrylic dome. Tolland then emerges from the sub.

Meanwhile, Rachel heads inside the ship to transmit as much evidence as she can in case she doesn’t make it out alive. She inserts all the evidence of the meteorite fraud into a fax machine. Knowing that communications are jammed, she programs the machine to redial continuously until it can transmit and then heads back to the main deck.

One hundred sixty miles away, Gabrielle, now logged into Senator Sexton’s computer, discovers scanned images of large, illegal campaign contribution checks deposited in offshore accounts.

The Kiowa helicopter, with the controller now aboard, hovers over the Goya. The pilot, Delta-One, and the controller are stunned to see Delta-Two held captive in the Triton’s claws and Delta-Three bound on the deck with Rachel holding a gun on him.

Rachel bluffs to the controller that she has already told an NRO analyst named Jim Samiljan about the fraud. The controller orders the radar jammer disabled to call the NRO and verify. The brief window allows Rachel’s fax to transmit successfully. Rachel demands that the helicopter back off, threatening to kill the remaining soldier. The controller agrees to come down, unarmed, to talk. The helicopter lands, and the controller steps out, revealing himself to be NRO Director William Pickering.

In the Oval Office, President Herney learns that Marjorie Tench is dead after having gone to meet the now-missing Pickering. Herney recalls that Pickering had previously gathered incriminating evidence against Senator Sexton—including financial records and photos of his affair with Gabrielle—and anonymously sent it to Tench, but Herney had forbidden Tench to use it. He’s then informed that a distraught Ekstrom needs to speak with him again immediately.

On the deck of the Goya, Pickering explains that he faked the meteorite to save NASA from being privatized by Sexton, which he considered a national security threat. He reveals that his NRO team discovered unique geology—including chondrules and fossils—while covertly working in the Mariana Trench and then took an existing rock from there, charred it with an expander cycle slush-hydrogen engine to simulate a fusion crust, and inserted it beneath the Milne Ice Shelf. He insists that NASA and the president are innocent and asks Rachel where she sent the fax. Meanwhile, Delta-One finds the fax machine in the ship’s lab, retrieves the destination number—Sexton’s office—and confirms to Pickering that Tolland’s gun is empty.

Sexton arrives at his office and confronts Gabrielle in the hallway, suspecting that she was inside. He returns to his office and asks Gabrielle to check the fax machine, and she brings him Rachel’s fax proving the meteorite fraud and containing her plea for help. Sexton then receives a phone message from Pickering warning him not to share the information or else Rachel will be killed. Ignoring Gabrielle’s pleas to protect his daughter, Sexton makes 10 copies of the evidence, seals them in envelopes for the press, and dismisses Gabrielle.

Rachel and Tolland stand together before Delta-One on the deck of the Goya, holding hands for comfort. Tolland privately recalls a dying Celia asking him to promise that he would find love again. Tolland had thought this impossible until he met Rachel. Rachel wishes to herself that she could hug Tolland but thinks they’re fated to die.

Delta-One forces Rachel to stand on top of the Triton submersible as “biological collateral” while ordering Tolland to release Delta-Two. Tolland covertly signals Rachel to jump inside the sub through its open hatch. As she does, Delta-One opens fire, with ricocheting bullets slamming the hatch shut. Tolland releases the ship’s anchor, causing the damaged Goya to list severely. The idling helicopter slides down the deck; Delta-One jumps in and tries to take off, but the rotors hit the Triton’s winch cable and shatter. The chopper crashes into the sea. The damaged winch cable then snaps, and the Triton, with Rachel trapped inside, plunges into the ocean.

Gabrielle begs Sexton not to risk Rachel’s life by releasing the faxed information. Sexton, fixated on the political victory, ignores her pleas and threats. He prepares to leave with his 10 envelopes of evidence for the media. When Gabrielle tries to call the White House, Sexton slaps her across the face and threatens her. Gabrielle leaves the building in a taxi, crying.

The Triton should ideally have been bobbing on the surface, but Tolland is shocked to watch the submersible sink. He takes off his shirt and flings it in the air to distract Pickering, who shoots at the garment. Tolland jumps into the water to land on the Triton, pounding on its glass to tell Rachel to get out.

Meanwhile, underwater, Rachel feels the immense pressure building inside the sub. She sees Tolland banging on the dome from outside, signaling to her to turn the wheel to the hatch so that she can get out. Rachel turns the wheel from inside while Tolland twists it from the outside. The dial refuses to budge beyond a few inches, as the portal lid isn’t aligned properly with the aperture. Tolland panics, fearing that Rachel may not be able to make it out.

Far below, the sunken helicopter’s Hellfire missiles detonate against the magma dome, triggering a massive underwater volcanic eruption.

Tolland panics as the Triton now plunges under the surface. He forces himself to think why the sub is collapsing and examines the hull, discovering a small gap in the viewing window through which water is leaking into the sub, compromising its buoyancy. Tolland clambers to the surface to gather his breath and grab a high-pressure air cylinder. He inhales deeply and dives to the Triton, pumping air through the crack, hoping the internal pressure will blow the main viewing dome off its damaged seal.

As the high-pressure air floods the cabin of the Triton, Rachel is seized by a blinding headache. She watches Tolland pound on the window, gesturing something, but can’t understand him.

Trapped alone inside the sinking, pressurized Triton, Rachel suddenly realizes that Tolland is trying to blow out the hemispherical viewing dome. As the sub sinks deeper and tips backward, Rachel remembers her mother’s words during a childhood accident on a frozen river: “Kick with your feet!” (431). Inspired by the memory, Rachel lies on her back and kicks the dome with all her strength, breaking the seal. A torrent of water rushes in, and she’s violently ejected into the dark ocean, disoriented and unable to tell which way is up.

Meanwhile, the sunken Kiowa helicopter’s Hellfire missiles detonate when the megaplume smashes the chopper against the magma dome below. Tolland, who had resurfaced for air and dived again, sees the flash of the explosion, which illuminates Rachel in the water just below him. The explosion rips open the magma dome, causing the underwater volcano to erupt. This creates a massive pillar of steam that forms a powerful, intensifying whirlpool, sucking the surrounding ocean downward. As this new danger forms, Tolland swims desperately toward Rachel and grabs her hand.

The temporary corkscrew effect of the explosion has the unexpected side effect of pushing Rachel and Tolland to the surface. They emerge as a Coast Guard Osprey arrives. The crew, investigating an explosion, have already rescued a wounded Corky from the water. They winch Rachel and then Tolland aboard. As Tolland is lifted clear, the whirlpool reaches the surface. They watch as Pickering and the Goya are sucked into the vortex and destroyed.

Senator Sexton holds a press conference at the Washington Monument, promising the media the scandal of the decade. Rachel arrives and privately pleads with him not to release the information, but he dismisses her. Gabrielle, wearing a borrowed cashmere coat, mohair beret, and ABC press pass, intentionally knocks Sexton’s envelopes to the ground and swaps them with a duplicate set containing sexually explicit photos of Sexton and Gabrielle retrieved from ABC. Unaware of the switch, Sexton distributes the envelopes. Instead of evidence of the NASA fraud, the press finds the photos. Humiliated, the senator is confronted by both women.

In the Oval Office, President Herney thanks Gabrielle for her actions. She has decided to leave Washington for a while. Herney offers her a future position on his staff and tells her that there’s no substitute for the truth. He then walks into the Briefing Room to address the nation and admit NASA’s mistake.

Rachel awakens late the next night in a White House bedroom. She learns from a news report that Herney’s honest confession about the meteorite, combined with her father’s sex and financial scandals, has secured Herney’s chances for reelection. A Secret Service agent informs her that Tolland is awake in the Lincoln Bedroom. After the agent diverts a visiting Corky to the kitchen, Rachel joins Tolland. He surprises her with flowers and a joke gift of goldfish. They embrace, and the two begin a romance.

Aboard a NASA transport jet, Ekstrom oversees the disposal of the fake meteorite. The massive rock is dropped from the plane and plunges into the Atlantic Ocean. It sinks for 12 minutes before crashing into the muddy seabed, where it’s briefly inspected by a deep-sea creature before being left alone in the darkness.