In the future, water has covered much of the Earth due to the effects of global warming. The orphaned Maia Mizuki, 15, just graduated from middle school and has already applied for employment in the elite paramilitary Ocean Agency, part of the futuristic world government. Only the best, most intelligent, and physically fit students are eligible for admission. Maia, the series' protagonist, is set to become one of the few. But her ideal life quickly falls apart. To her disappointment, Maia unexpectedly fails her entrance exams. Making matters worse, she promptly gets evicted from her house, pick pocketed, taken hostage, then shot. She is "saved" by two women (Rena and Shizuka) that are part of an unorthodox help-for-hire organization called Nereids (inspired by the Greek mythological Nereids ). With nowhere to go, Maia joins up with Nereids, taking jobs from capturing wanted criminals to chasing stray cats, often with unexpected results. Gloria and Yu later join up with Nereids. "Daphne" in the title refers to a subplot that starts midway into the series and eventually become important to Maia. "Brilliant Blue" refers to the fact that this is a world covered by water with almost no land. The world consists of vast oceans, a few islands, and floating cities.

The story is set in 1955 in Kokuga, Hofu City, Yamaguchi Prefecture. One thousand years ago it was the site of the ancient capital, Suo no Kuni, and traces of the Heian Period (year 794-1185) are passed down to us in the form of ruins and historical place names. The protagonist is Shinko, a third grade elementary school student, who was born and raised in one of the town's venerable families. She is a little girl whose characteristic is a strange curl on her forehead (she calls it her "Mai Mai"), and her love for playing in the fields. On the other hand, her secret joy is to imagine and to daydream about the world of one thousand years ago. Her fantasies travel far into the days of the Heian Period... One day, a girl called Kiiko transfers from Tokyo and enters Shinko's class. This girl from the big city has difficulty feeling at home in this small town, but gradually her friendship with Shinko deepens. Before long, the two of them become engulfed in a strange incident of one thousand years earlier...?!

Daru, a cherished handmade stuffed toy, gets lost and separated from its owner one day when at the airport. Determined to find her again, Daru sets out on a journey around the world in search of her. As time passes, the girl begins to forget about Daru. Will Daru be able to find and see his beloved owner again?

Unusual things have been happening in Moominvalley. Moomin, Sniff and Mee leave for the Observatory on the Lonely Mountains to confirm the Muskrat's words: a comet is about to hit Moominvalley and destroy everything. On the way they meet Snufkin, the Hemulen and the Snorks and experience many adventures.