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The game is played from a top-down perspective and is a turn-based tactics title in which players issue commands to a squad of human soldiers to eliminate the hostiles in a map and depending on the mission, complete secondary objectives. Players can freely explore the map without being confined to a grid. Each character can perform three actions, such as taking cover, shooting enemies, or remain in overwatch to shoot any moving enemy in their line of sight. When an enemy unit loses most of its health, a friendly unit can move in and execute the downed enemy, which gives all units an additional action point. Players need to throw grenades to destroy erupting Emergence Holes which spawn more Locust enemies. If a friendly unit sustains too much damage, players may need to revive them, though they will still lose a significant portion of their health. The game has five distinct character classes, with each having its own unique abilities. The characters can be extensively customized with mods, armours, and they can acquire new skills after they level up. A permadeath system will be featured in the game. Other than the two central characters, other friendly units are procedurally generated and should they die in combat, their deaths will be permanent.

One year after Emergence Day, when a subterranean race of creatures known as the Locust Horde emerged on the surface in a campaign to kill every human on the planet of Sera, Coalition of Ordered Governments leader, Chairman Richard Prescott, orders all major cities outside the Jacinto Plateau to be incinerated by the Hammer of Dawn. In addition, the Chairman had sent mop-up detachments in key-cities to eradicate the surviving Locust. One of the mop-up crews was Alpha Squad, stationed in Aldair City. Among them is Pendulum Wars hero, Sgt. Gabriel Diaz, who had demoted himself to working in the motor pool. Mere hours before the Hammer Strikes, he receives orders from Chairman Prescott and Major Sid Redburn to retrieve classified intel files from the CIC building. Sgt. Diaz and Major Redburn find the files that reveals to be about a Locust scientist named Ukkon, who has been responsible for the various creatures the Locust have been using as instruments of war. The Hammer of Dawn then destroys the city of Aldair, but Sgt. Diaz and Major Redburn survive. However, Ukkon destroyed the army base and killed everyone. Prescott then orders Diaz to assassinate Ukkon and is granted the rights to do so by any means possible. In need of soldiers for the fight, Sgt. Diaz and Major Redburn rescue another mop-up squad, Echo-Five, but discover that Ukkon has been killing the mop-up crews. After rescuing a Stranded group, a militia of civilians who survived the Hammer Strikes, they also join Alpha Squad. Their leader, Mikayla Dorn, is aware of Ukkon and escorts Sgt. Diaz and Major Redburn to the city of Claybourne where Ukkon frequents. Upon spotting Ukkon, Mikayla manages to shoot Ukkon in the mouth and apparently killed him. Ukkon, however, comes back to life and immediately repairs the damages done to his face. Sgt. Diaz then realizes that the COG is once again holding secrets like before, and fears that they will get them killed.