Plot
On August 23, 2023, a United States Marine Corps Force Recon unit is deployed into New York City to extract former Crynet employee Doctor Nathan Gould, who may have vital information on combating the Ceph, the alien race that is trying to destroy humanity. However, the Ceph sink the submarine transporting the unit, killing everyone but Force Recon Marine "Alcatraz", who is left mortally wounded. Delta Force Major Laurence "Prophet" Barnes saves Alcatraz and kills himself to allow his Nanosuit to assimilate and revive Alcatraz. In a recording, Prophet reveals that he had been infected by the Manhattan virus, and asks Alcatraz to continue his work against the Ceph. Believing Alcatraz is Prophet, Gould contacts Alcatraz and asks him to meet up at Gould's lab. CELL forces, led by Commander Dominic Lockhart, attack Alcatraz, believing him to be Prophet.
On his way to Gould's laboratory, Alcatraz collects tissue samples from the Ceph, which cause strange reactions within his Nanosuit. Alcatraz meets with Gould, who becomes aware of Prophet's death, and explains that the suit has been rewriting its own code after absorbing the Ceph's tissue. He speculates that the suit is creating an antibody for the Manhattan virus, and they decide to scan more samples at a Crynet base on Wall Street. The scans are cut short when CELL forces led by Lockhart and Lieutenant Tara Strickland ambush them.
As they attempt to transfer Alcatraz to their headquarters, the Ceph attack the CELL personnel. Additionally, a massive alien spire rises from the underground, releasing a spore-based bioweapon that kills most CELL troops in the area. Alcatraz's nanosuit further adapts the spores, but malfunctions, and is rebooted remotely by Crynet director and Hargreave-Rasch Biotechnologies co-founder Jacob Hargreave. Hargreave contacts Alcatraz, claiming to have knowledge of the Ceph, and to have designed the Nanosuit based on stolen Ceph technology to be used as a defense against the aliens. Hargreave directs Alcatraz to another Ceph spire to conduct an experiment for him.
On the way, Hargreave reveals to Alcatraz that the Manhattan virus had been spread by the Ceph, to clear out the entire human population from Earth. The Manhattan virus would cause all infected humans to melt down into a liquidated mass, which could then be stored and disposed of. Upon reaching the alien spire, Alcatraz attempts to interface the Nanosuit's systems with the aliens' technology, but fails. Meanwhile, the US Department of Defense rescinds CELL's authority over Manhattan and deploys Marines in their place under the command of Colonel Sherman Barclay. The American forces order an air strike on the city's flood barrier, in an attempt to drown the aliens out of lower Manhattan. Washed away by the resulting wave of water, Alcatraz is found in Madison Square Park by a squad led by Alcatraz's squadmate Chino, who survived the submarine's destruction. The Marines enlist his aid in evacuating civilians to Grand Central Terminal, the city's primary evacuation point.
Hargreave asks Alcatraz to take a detour to the Hargreave-Rasch building, to find a stabilizing agent to facilitate the Nanosuit's analyzing process. Ceph interference causes this to fail, with Hargreave telling Alcatraz to help evacuation efforts at Grand Central. At the terminal, Alcatraz is reunited with Gould, who had somehow escaped Strickland. Grand Central is overrun by Ceph forces, but Alcatraz holds them off long enough for the evacuation to succeed, and he escapes the building.
Alcatraz is tasked with defending another evacuation point at Times Square, and this time manages to repurpose the alien spores to be lethal to the Ceph, destroying all Ceph in the area. With the evacuation complete, Gould instructs Alcatraz to head to Roosevelt Island, to infiltrate a Crynet complex named "The Prism", where Hargreave resides. Alcatraz foils Lockhart's attempts to ambush him, and kills him in the process. However, he is then betrayed and captured by Hargreave, who wants the Nanosuit for himself, to continue the mission in person. Hargreave attempts to remove the Nanosuit from Alcatraz's body, but the Nanosuit resists its removal, having assimilated with Alcatraz. Alcatraz is then rescued by Strickland, who reveals herself to be an undercover CIA operative responsible for Alcatraz's deployment. Strickland instructs Alcatraz to capture Hargreave.
In Hargreave's private office, Alcatraz discovers Hargreave's body in a vegetative state stored in a cryonic chamber. Hargreave reveals to Alcatraz that he had been communicating with him through an advanced computer system, having been injured in an encounter with the Ceph at Tunguska. Hargreave gives Alcatraz a Nanosuit upgrade, allowing it to fully interface with the Ceph, as the Ceph invade the island. Hargreave triggers the self-destruct system of the complex, and orders the remaining CELL forces to aid Alcatraz's exfiltration. Alcatraz escapes the complex, and reunites with Gould, Strickland and Chino on the shores of Manhattan.
Alcatraz is notified by Barclay that STRATCOM has just authorized a tactical nuclear strike on Manhattan Island. Thus, Alcatraz has a short period of time to end the conflict with the Ceph before the missile is launched. Alcatraz and his comrades make their way toward the center of the alien infestation, and spot a massive alien "litho-ship" rising out of the ground beneath Central Park. Alcatraz assaults the floating section of Central Park, and makes his way to the alien spire at its center, which serves as a dispersal point for the alien spores. Alcatraz successfully turns the spire's bio-weapon against the Ceph, causing the death of all the Ceph in the city.
After some days, the city begins to recover with the help of Gould, Strickland, and the US military. Alcatraz, while unconscious, communicates with Prophet, whose memories, experiences, and personality had been stored in the suit. Prophet tells Alcatraz that, while the mission in New York is a success, the Ceph, who had been present on Earth since prehistoric times, had built constructs globally. The Nanosuit then assimilates Prophet's memories into Alcatraz. The Nanosuit then receives a broadcast from Karl Rasch, the other founder of Hargreave-Rasch Biotechnologies, asking for his name. Alcatraz replies: "They call me Prophet.".
