2150 A.D. The battle with the Festum, the silicon life-forms from distant outer space, had reached a new dimension. The North Polar Meir that was crushed during the First Azure Operation had dispersed its fragments all over the world. They all started activity on their own as independent Meirs. Most of the Meirs harbored hatred towards humanity and challenged a fight, however, a portion of the Festum chose coexistence with mankind. Amongst the crossfire, the Ryugujima island alone disappeared from the forefront of battle and continued its silence. The island had gained a means to converse with the Meir since their encounter with Misao Kurusu two years ago. The children of ALVISS had been searching for a way to understand the enemy as they prepared for battle. And now, once again, further evolution was about to befall the island. A girl that understands the language of the Festum, and a girl protected by a Festum. When the two meet, the doors to a new universe opens.

Tatsumiyajima is the central island in the middle of a small cluster of islands, in a sleepy backwater of the Japanese isles. Not much happens there, and the island's young people go to school knowing that their lives are likely to remain peaceful and undisturbed. Or so they have been taught...but the truth is different. The fate of mankind is on the line, and Tatsumiyajima is the last line of defense against a hostile and incomprehensible enemy. At the center of it all, fighting for Humanity's continued existence, is the giant robot Fafner, the dragon that guards this final treasure of mankind.

Follow the adventures of three ordinary girls as they make life’s awkward moments a thousand times worse. Along with a colorful bunch of classmates, they learn their most important lessons the hard way. Meanwhile down the street, a pocket-sized professor makes life difficult for a robot who just wants to be normal. But normal is the last thing you can expect in a town where salmon falls from the sky. In fact, the only thing you can count on is your friends, but even they are totally weird.

A week before Christmas, Kyon wakes up in a world where the SOS Brigade doesn't exist. Mikuru and Yuki don't recognize him, and Haruhi and Itsuki seem to have vanished.