The game is a Third-Person Shooter like its predecessor. The player has to kill enemies and complete levels, and this will result in completion of the game. The game features Morality moments, where they can make choices that effect the game.
Tyson Rios and Elliot Salem, Contractors of Trans World Operations, are sent on a mission to Shanghai to meet JB. JB tells them he was also a former SSC Operative, and leads them to a weapon and equipment cache concealed in a dumpster. They then proceed placing beacons in key areas in the city, as well as fending off concerned Security Guards.
Shanghai is then attacked, and Rios and Salem only just escape, and fend off mercenaries hired to kill them. Alice contacts them again, to inform them she is trapped in the South African Embassy. They fight through mercenaries and free civillian hostages, then they reach the Embassy and free her. They then fight through Underground tunnels until they reach Shanghai Zoo, where an Employee guides them to the exit, where they rescue a trapped worker on the way. Alice then contacts them to reach a Communications Tower to signal for help. They find the tower to contain an empty room, and them go to a balcony, which subsequently collapses, with Salem being knocked unconscious. He wakes up in hospital later, where Doctor Wu asks the two to help evacuate patients. After that, they head to the Mall, where they end up captive until freed by Breznev. Breznev tells them that three bombs destroy the communications tower, and the pair plant them, before leaving Breznev. A helicopter tasked to extract them is shot down by Anti-Aircraft Weaponary.
The pair then decide to kill the leader of the the 40th Day Initiative, Jonah Wade. They track him down to a heavily fortified temple. They rescue civilian hostages, who then arm themselves and assist the pair in killing Initiative members at the Temple. They reach the inner areas of the Temple, where they meet Jonah, who claims he is getting rid of the worlds moral decay, and threatens to detonate a nuclear bomb in the heart of the city.
He says they have to do an Act of Sacrifice, or defeat him and his army, which will result in the bomb detonating. They find out the nuclear bomb was a hoax. If the player killed his partner, they mourn their loss. If they killed Jonah, it shows him claiming he took inspiration from the Bible.