The main star is Zero, Aero’s rival from the previous games. During the events of Aero the Acro-Bat 2, Zero receives a telegram from his girlfriend Amy telling him that an evil lumberjack named Jacques Le Sheets is deforesting their homeland Stony Forest to produce counterfeit money and has also captured her father. Ignoring Edgar Ektor’s protests, Zero decides to put a stop to Le Sheets. Upon arriving at the island, Zero’s plane is shot down and crashes on the beach, so he starts making his way to the forest on foot.
During his journey, Zero learns that Amy has also been captured after an unsuccessful attempt to save her father by herself. At the paper factory, Zero fights Le Sheets and pursues him on a flying ship. Aboard the ship, Zero finds that the mastermind is none other than Edgar Ektor. After defeating Ektor with Amy’s assistance, the two squirrels parachute safely away, while Ektor’s ship crashes into a cliff.