What is supposed to be a vacation for sonic, Manic and Sonia turns into a battle to save Mobius when Robotnik attacks with his newest weapon - The Flying Fortress. Sonic investigates the ship thinking the weapon can be destroyed by removing its reactor, however his efforts fail and he goes to Knuckles for help, because he believes the weapon is powered by the Chaos Emerald. Knuckles agrees to aid him suppressing the fear that the Floating Island will be left unprotected. Knuckles and Sonic locate power source only to have it taken by Sleet and DIngo before the Hedgehogs can reach it.