After the battle of Gem City Annie Reid has fled to the forest with a contingent of local militia while Perky Whittier has been captured and finds herself at the Cyclone research and development base Camp Phanes, to be a part of an experiment called Project X. Annie is determined to find Perky, and Perky is determined to wreak havoc on Project X. Meanwhile, Discovery City is under siege by the New World Order's monstrous battleship, Colossus. Aboard the Colossus, a clone girl and product of the previous iteration of Project X, Sybil Ludington, has been tasked to infiltrate the citizenry of Discovery City. Bearing a particular hatred for the Cyclones, Sybil sets of on her assignment. When the whole group begins to work against the Cyclones the threat levels rises.