Pinky and The Brain have a new plan to seize world supremacy. After a TV report on a new meteorological station in space, Brain comes up with a plan to modify the station in order to control the weather and thus bring the powerful of this world to their knees. As usual, the plan is put down on paper and Brain soon notices that it is impossible to execute this plan in one evening. After all, this is... the Masterplan. Unfortunately, the plan is stolen overnight by two lab rats. Help Pinky and The Brain recover the plan, leading them through 20 levels in 5 different worlds collecting the pieces of the plan that Roofus and Doofus, the two lab rats, lose on their way. Follow them through the laboratory in a submarine, a jeep and even into space.