The game takes place in the fictional city of Neo City in 1992. There is a center of operational counteraction to organized crime, called "Contra Force", headed by a man named Burns (Burns). The operatives are tasked with destroying the criminal syndicate called "D.N.M.E". Burns receives a call from someone named Fox, an informant, who reports that unknown persons are threatening the head of intelligence. Burns sets up a meeting with the informant to find out more details. However, when Burns arrives at the port where the meeting was scheduled, it turns out that Fox is already dead. Burns and his squad are suddenly attacked by armed bandits. Now the heroes must clear the city from the terrorists.

The game has many innovations compared to previous games in the series:
- Appeared partner, controlled by a computer.
- The main character is now possible from four characters, which differ in a set of weapons, jump height and running speed;
- Change of weapons occurs by accumulating bonuses;
- Appeared homing missiles;
- The environment has become more interactive: now the heroes can destroy individual devices, boxes and some items;
- The influence of atmospheric phenomena: the wind blows towards the character running along the wing of the aircraft.