When you look up at the sky, what do you see? A blue sky? Freedom? A hopeful future? The people of Tokyo see none of these. Instead, an ominous alien mothership looms overhead, engulfing the city skyscape. Three years ago, they came. The arrival of the "Invaders" sparked the greatest war humanity had ever faced—one that threatened to end the world. The Japanese government scrambled to fight the Invaders. Weapons were mass-produced, sparking controversy and pacifist movements. That day, everything changed. And yet, nothing has changed. Kadode Koyama and Ouran Nakagawa live their final days like they always have: going to school, playing with friends, and doing what any carefree high school girl would do. As they grow up they come to learn what it truly means to be an adult, in a world where adults seem to be demons who only deceive and destroy. They come to learn the real threat to humanity is not the Invaders, but humanity itself.

The year is 2040 and the galaxy is flourishing with several colonies and advanced technology. AI is near perfection and the current top idol is the near-completed Virturoid Idol Sharon Apple. All that is missing are her actual feelings, which instead are supplied by Myung Fang Lone. Sharon's debut concert is on planet Eden, where at the same time, fighter pilots Isamu Dyson and Guld Bowman battle over air superiority for the "Supernova Project." Isamu, Guld and Myung were once childhood friends, but after an accident seven years ago, they went their own separate ways. With Myung back in the picture, the old disputes are once again awakened. And when an unstable and illegal AI technique is installed in Sharon, the situation is worsened.

Koji Nanjo, a young rock star, falls in love with soccer player Takuto Izumi. Koji eventually learns that Izumi's mother killed his father out of severe and intense love. Izumi took all the guilt for his father's murder and refuses to go pro because of fear that his past will be discovered by the media. Izumi detests Koji's company and encouragement and severely dislikes the attention from the press, but Koji cannot stay away for he soon realizes that his love for Izumi is very similar to the love that Izumi's mother felt for his father.

Shin Kazama, tricked and forced into flying for the remote country of Aslan, can only escape the hell of war by earning money for shooting down enemy planes or die trying. Through the course of the series, Shin must deal with the consequences of killing and friends dying around him as tries to keep his mind on freeing himself from this nightmare.