The game begins in 2020 when North Korean Forces led by General Ri-Chan Kyong take control of the Lingshan Islands. A team of American civilian archaeologists, led by Dr. Rosenthal, send out a distress call indicating that they have discovered something that could change the world. Thus Raptor Team is dispatched to the islands, with the core mission of evacuating them and securing any valuable information that they have. The team consists of Nomad, Psycho, Aztec, Jester and team leader Prophet (all under code names); they are outfitted with Nanosuits, which help protect them from gunfire and explosions, as well as giving them superhuman strength and abilities. As they perform a high-altitude jump onto one of the islands, an unknown flying entity disrupts the jump by smashing into Nomad, and the team is separated. The crash deactivates Nomad's Nanosuit and destroys his parachute, but he is saved because he lands on water and his suit absorbs the impact of the landing. After he makes his way to shore, Prophet is able to reset Nomad's suit remotely, restoring its normal function.
As Raptor Team regroups after the jump, Aztec is killed by an unknown entity. When the team finds him, they discover that whatever killed him also killed and dismembered a nearby squad of KPA. The remaining members of Raptor Team proceed with the mission. Along the way they discover the hostages' boat frozen on a hill near the coast of the island. They also get their first look at the aliens who have been attacking their team, when a flying alien machine sneaks up on them and snatches Jester, killing him shortly thereafter. The first hostage the team rescues turns out to be a CIA agent who was sent to monitor Dr. Rosenthal's work. In the jungle, Nomad finds another hostage named Badowski dead with ice shards in his back, as the KPA battle an alien machine nearby. After Nomad regroups with Prophet, Prophet is suddenly snatched by another flying machine, which flies away with him in its grasp. Shortly after, Nomad is contacted over the radio by Major Clarence Strickland of the American military asking if he wishes to abort the mission since most of his team has been killed or missing; Nomad refuses, saying that he can still complete the mission. A day/night cycle operates during the course of the single-player campaign.Nomad makes his way to Dr. Rosenthal's research complex, where he has found a rare fossilized artifact predating humanity by two million years. The partially excavated artifact resembles one of the flying machines (designated "exosuits") that has been attacking the team. Rosenthal also references other discoveries of similar artifacts in Afghanistan and Siberia, suggesting that the aliens have a global presence, and are not just confined to the island. While Rosenthal is running a scan on the artifact, it emits a powerful energy pulse that freezes Dr. Rosenthal solid. Nomad's Nanosuit is able to maintain his internal temperature, saving his life. Nomad then rendezvous with a VTOL, after eliminating a Nanosuit-equipped four-man KPA special forces team near the landing site. He notifies his superiors about this, because the U.S. military had hoped to prevent the Koreans from acquiring Nanosuit technology.
The U.S. military then begins a full-scale invasion of the island, led by Major Strickland. As the U.S. forces continue to the main excavation site, the central mountain on the island begins to fall apart, revealing a huge alien structure inside, which is nearly the size of the mountain itself. Nomad enters the excavation site at the mountain's base, but is captured by Kyong's men. Kyong deactivates Nomad's Nanosuit, and Nomad watches, helpless, as Kyong shoots one of the hostages in the head and then detonates explosive charges to open the structure. An energy pulse emanates from the structure and kills Kyong's men; the pulse also reactivates Nomad's Nanosuit. Kyong, also wearing a Nanosuit, attacks Nomad, until Nomad is able to kill him. As the mountain continues to collapse, a VTOL evacuates the last hostage, Dr. Rosenthal's daughter Helena, but is unable to rescue Nomad.
Nomad gets trapped and decides to continue into the alien structure. It soon turns into a zero gravity environment. Nomad uses his hydro-thrusters to maneuver and encounters hostile sentient aliens. He also sees a possible invasion force consisting of many Alien machines. Nomad manages to escape, but the structure creates a massive sphere of energy that freezes everything outside to -200°F (-129°C). Once outside, Nomad is attacked by various Alien machines before finding Prophet. Prophet was able to engineer a weapon using the aliens' technology, the Molecular Accelerator (MOAC). Prophet's Nanosuit malfunctions, requiring him to frequently stop and recharge using heat sources, such as the burning wrecks of military vehicles. The two leave the ice sphere and rescue Helena, whose VTOL has crashed. Prophet leaves with Helena on another VTOL. At the U.S. evacuation point, one of the last VTOLs rescues Nomad from an unstoppable quadrupedal alien exosuit. Just as the exosuit is about to destroy the VTOL, Major Strickland draws its attention by firing at it using a mounted machine gun and the exosuit kills Strickland instead. As they leave the island, the pilot is killed and the engines are damaged. Nomad flies the crippled VTOL back to the USS Constitution (CVN-80) carrier strike group while fighting off aliens along the way.
Once there, he meets up again with Psycho and is then debriefed by Admiral Richard Morrison who explains that a nuclear strike has been ordered against the ice sphere. Helena warns him that the aliens might absorb the energy, but the Admiral ignores her. Prophet flies a VTOL back to the island against orders. Despite Prophet's departure, the nuclear missile is launched at the ice sphere. The explosion causes the ice sphere to expand and prompts a massive alien counterattack.
Nomad is ordered to repair one of the carrier's damaged nuclear reactors. The Nanosuit is resistant to high levels of radiation, although prolonged exposure proves deadly. While Nomad is in the reactor room, Helena sends an experimental signal through Nomad's suit that causes several alien machines to absorb too much power and overload, destroying them. As Nomad returns to the flight deck, Admiral Morrison is killed and Nomad takes the prototype TAC-Cannon. On the flight deck, Nomad fights an alien exosuit similar to the one that killed Strickland. A massive alien warship then emerges from the sea, and Helena manages to deactivate its shields by sending a signal through Nomad's Nanosuit. Nomad then uses the TAC-Cannon to destroy the alien warship, which falls on the carrier and begins to sink it. Nomad runs across the flight deck and jumps off the carrier into the waiting VTOL, which is piloted by Psycho. As they fly away, Helena is nearly pulled out of the aircraft by the energy field created by the destroyed alien warship. Psycho then receives a transmission that there is another Carrier Strike Group en route to the island and suggests meeting them. Nomad protests, claiming that since they now know how to defeat the aliens, they need to continue fighting. A transmission from Prophet, who is inside the energy field on the island, is then received. The VTOL is then seen turning around and heading back to the island.
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