Set in 1999, young Wakatake Mari, transfers to an all girl boarding school named Kaihō Academy. Mari was the only person left in a bizzare event that caused 800 residents of a solitary island to turn up missing 5 years prior but has no memory of the event. Mari is lonely and hostile and wants nothing more then to leave the school.

Her roommate in the strange new school is Senkōji Hagino, popular, pretty, smart and athelic, who has a strange secret of her own. She is the pilot of an alien vessel called Blue who may be responcible for the disapearence of the people of Mari's island. Hagino was sent to earth on a reconnaissance mission prior to an invasion and is an alien herself.

At first their relationship is strained, but as Mari starts to emerge from her self imposed isolation, Hagino starts to question her mission.

Based on the manga Blue Drop by Akihito Yoshitomi.