On 2245, an intruder broke into the hangar and stole the latest IS. 7 teenagers race against time to chase the figure to the past to stopped the figure from eliminating their father. However, they must enroll in the academy in order to hide their identities as well as their IS which was the 9 generation being developed by their eldest brother. Will they be able to stop the figure?

A few month has past since the fall of Messiah. Lacus has became the Chairwoman of the Supreme Council while Kira became ZAFT commander and Athrun became admiral of the Orb forces. What will happen if an alien was recovered near the PLANT. Will they be able to fend off the invasion? An unknown organisation with the most advanced technology appeared out of nowhere came to aid them.