In the present day, before the start of 7 Seeds, when astronomers predict that Earth will be hit by a meteorite, the world leaders met to develop a plan for human survival, called the Seven Seeds project. Each country would cryonically preserve a number of healthy young people, which would allow them to survive devastation of the impact. After a computer determines that Earth is once again safe for human life, it would revive each group.
The Japanese government created five groups of survivors named Winter, Spring, Summer A, Summer B, and Fall. Each group consisted of seven members, who were not told what would happen before being put in cryonic preservation, and one adult guide who is trained in wilderness survival. These groups were scattered across Japan: the Summer groups in southern and northern Kyūshū, Fall in western Honshu, Spring in cental Honshu near Tokyo, and Winter in Hokkaidō. The project also prepared sealed caches containing seeds and instructional books near the "seven Fuji". These seven Fuji are not related to the famous Mount Fuji, but are regional landmarks also named Fuji:
* Bungo Fuji in Ōita Prefecture is Mt. Yufudake, where the cache is marked by a statue of the Buddha Dainichi.
* Ogino Fuji in Kanagawa Prefecture is Mt. Kyogatake, where the cache is marked by a statue of Monjubosatsu (the bodhisattva Manjusri).
* Kobe Fuji in Hyogo Prefecture is Mount Futatabi of the Rokkō Mountains.
* Natori Fuji in Miyagi Prefecture is Mt. Taihaku, near Sendai.
* Akan Fuji in Hokkaidō is Mt. Meakandake, where the cache is marked by a statue of Senju-Kannon (the goddess of mercy).
7 Seeds follows these five groups, as they are revived an undetermined time after the impact and come to turns with survival in a Japan that has greatly changed.
Upon waking on a sinking ship, a young girl finds herself in the company of strangers. Forced to escape certain death, the four find themselves stranded on a deserted island. In order to survive, they need to get over their differences and try to figure out what happened as none of them seem to have any recollection of ever boarding a ship...