
The game is set in New York City as a virus infects people and the military attempts to put an end to it. The protagonist of the story is named Alex Mercer, who has enemy-absorbing andshapeshifting powers. He can take memories, experiences, biomass and physical forms of enemies through absorption. Alex can also shapeshift into more specialized forms for attack, defense or sensory enhancement. All of these together are intended to give players multiple ways to complete their objectives. Parallel to the game's storyline is the ability to play the game as a sandbox-style video game giving the player free roam of Manhattan

Among the enhanced parkour feats Alex can perform are running up the sides of skyscrapers, jumping hundreds of meters, gliding through the air and sprinting at extreme speed indefinitely. Falls do not damage the player no matter the height, but greater ones will visibly deform the ground. Alex may use various weapons, seize and control military vehicles including helicopters, perform various melee attack without shapeshifting, as well as more gymnastic moves such as air combos, sliding along the ground using any human enemy's body and a high-speed rolling cannonball attack. Alex can regain health by consuming biomass, though over time he can regenerate to a limited degree out of combat.

