A massive series of wars eventually forms a worldwide alliance superseding the UN with the ANA on a mission to promote the World Peace Act. However their extreme measures give way to acts of terrorism. In response, ANA seizes power and repels every effort to circumvent them. Eventually the ANA is abolished, but terrorists under the name FM now have the opportunity to rise and take over. TEAM BLUE is put together to act against the FM threat.

In Brain City, the player will have a number of missions. Each mission has the player assign a number of special forces each with their own statistics and inventory. Movement of the special forces has a limited number of steps, before the player's turn ends and both enemies and NPCs act. During the player's turn enemies can be attacked and killed, items can be picked up