Young Sky Knight Aerrow and his squadron, The Storm Hawks, are determined to become an official squadron, but they will first have to prove themselves to the Sky Knight Council. Meanwhile, the Dark Ace and his squadron are sent by the evil Master Cyclonis to steal the Aurora Stone, the most powerful crystal in the world of Atmos.

The Storm Hawks join a mission to take back the Aurora Stone; though the team is instrumental in getting the stone away from Master Cyclonis, the members are not allowed to register as a Sky Knight squadron.

The Storm Hawks promise an old Sky Knight they'll rescue his granddaughter Dove, a prisoner in the clutches of Cyclonia. But when they sneak inside the Smelters of Terra Gale for the mission, they find Dove is anything but a damsel in distress. Rebel Ducks: Protectors of Terra Gale, until a Cyclonian invasion defeated the squadron. Several members were forced into exile, while the rest were imprisoned and made to work in the factories and smelters that now pollute the once-clear skies of their beloved home terra.

After losing a Phoenix Crystal to the "honorable" Rex Guardians, the Storm Hawks challenge them to a series of events to get it back. However, in order to win, they will have to do it without breaking their ancient rules. Meanwhile, the Dark Ace plans to steal the crystal, but will he succeed?

Junko worries that without his Knuckle Busters, he is worthless to the Storm Hawks. All the while, the Time Pulse that controls all navigation instruments is shut down.