The expansion introduces a new set of enemy aliens called the Chosen, three elite alien-human hybrid warriors tasked by the Elders to defeat XCOM and recapture the Commander: the Assassin, who relies on stealth and melee attacks; the Hunter, who uses a long range rifle that fires bullets that track their targets; and the Warlock, who uses psionic powers and can take control of several of the player's units at once.

As the game progresses, the Chosen gain new exclusive abilities over time, and eventually become able to launch a direct attack on the Avenger.

Each faction also provides covert ops missions in which soldiers can be deployed to obtain extra resources, delay the Avatar project, or gather info about the Chosen's strongholds, as well as other benefits.

Other new features include a revamped strategic layer and the "Bond" system, in which pairs of soldiers develop special abilities that are accessible when both are deployed during a mission, however, when a bonded soldier is killed, their partner may temporarily enter a "berserk mode", ignoring any player orders and attacking targets at random, or they may panic, becoming uncontrollable and fleeing from battle.

Six of the voice actors new in the expansion are known for their roles on Star Trek: The Next Generation: Denise Crosby, John de Lancie, Jonathan Frakes, Michael Dorn, Dwight Schultz, and Marina Sirtis.

As the game progresses, XCOM is occasionally attacked by the Chosen, three elite alien warriors with orders from the Elders to recapture the Commander.

[8] IGN's reviews editor Dan Stapleton praised the amount of variety War of the Chosen added to the mission objectives and campaign of XCOM 2.