Amamiku, daughter of terraformers who crashed their seed-bearing spaceship into one of Earth's less radioactive oceans, was placed in stasis by her parents before they perished. She emerged ten years later. Now ninety years after the crash, the fourteen-year-old girl lives alone within the wreckage. Her body resembles a sixteen-year-old's, while her face appears closer to twelve. She is accompanied by the small robot Pyron and the computer system Mayzamik. Having known only isolation, she has never met another human.

Her mission is to guard the seeds containing Earth's genetic code, continuing her parents' work to restore the planet's fertility when conditions allow. Her existence is discovered by surviving humans. After venturing too far from the ship, she is rescued by a submarine crew, an event igniting prolonged conflict. Amamiku faces repeated attacks from Glyptofane, a disembodied brain viewing humanity as a plague, and its robotic Gadom army. These assaults force her and the submarine crew into a series of escapes as they try to transport the seeds to the undersea city of Bachisfare. Glyptofane's relentless pursuit forms the central challenge to her planetary restoration goal.

Her name derives from Amamiko (or Amamikyo/Amamikiyo), a creator goddess in Ryukyuan religion associated with the Amami Islands.