Undercover GRE agent Kyle Crane is airdropped into Harran to retrieve a sensitive file stolen by Kadir Suleiman, who is using it for blackmail. Crane is bitten by an infected, though he is rescued by Jade Aldemir and taken to a survivor sanctuary called the Tower. Crane is introduced to Rahim Aldemir, Jade's younger brother, who then teaches him the basics of parkour. Crane learns that the Tower is being harassed by a gang of bandits led by a warlord named Rais who steals and hoards supplies from the GRE airdrops. This includes Antizin, a drug that slows the process of infection and suppresses its symptoms. Crane is tasked with reaching an airdrop containing the direly needed Antizin but the GRE instructs him to destroy the airdrop and instead buy the drug from Rais in order to confirm his identity. Crane reluctantly complies and lies to the Tower that the supplies have been looted.

Upset, Tower leader Harris Brecken tasks Crane with negotiating a deal with Rais. Upon meeting Rais, Crane is able to confirm that he is indeed Suleiman. Crane carries out a series of unethical tasks for Rais under the assumption that he will be rewarded with two crates of Antizin, but Rais betrays him by only giving him five vials. He later severs relations with the GRE when they halt the supply drops and refuse to help the Tower. Desperate to obtain Antizin, Crane and Jade raid Rais's storage facility but they instead find a cache of plastic explosives. Rahim attempts to use the explosives to bomb a Volatile nest, despite Crane's objection. Rahim is wounded, and Crane executes Rahim's plan and destroys all the infected in the nest. However, when he returns, he discovers that Rahim was actually bitten and had turned into an infected while Crane was gone, forcing Crane to kill him.

Meanwhile, a scientist at the Tower named Dr. Imran Zere, who was attempting to develop a cure for the virus, is kidnapped by Rais. Crane attempts a rescue but is also captured. Rais reveals that the file he stole contains proof that the GRE intends to weaponise the virus rather than develop a cure. In the process of escaping, Crane cuts off Rais's hand. Dr. Zere is killed after telling Crane that he had tasked Jade with delivering his research to scientist Dr. Allen Camden. As Crane searches for Jade, he learns that the Defence Ministry is planning to firebomb Harran in an effort to eradicate the outbreak, claiming that there are no survivors. Working with the Embers, a survivor group in Old Town, Crane tries to alert the outside world by setting off bombs in an apartment building in the pattern of a sad face, but a jet fires a missile which obscures the pattern. Crane then reactivates a radio tower and successfully alerts the outside world of survivors in Harran, thwarting the Ministry's plan. In a desperate effort to evade scandals, GRE contacts Crane to retrieve Dr Zere's research for them so they can convince the public they are working on the cure, in exchange they will extract him safely from Harran.