Subaru Natsuki finally gets to take a breather, but he does not waste any time as he prepares for a date with his beloved Emilia. He scouts the nearby village for the right dating spot, and with the help of the village children, he finds a wonderful location. With that, he is well prepared for his date! Unfortunately for Subaru, cold weather suddenly sweeps across Roswaal's mansion on his important day, leaving him with no choice but to postpone the date. Overnight, it becomes even colder and unbearable. Subaru must get to the bottom of this because, at this rate, his date will be the least of his worries.

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.

Texhnolyze takes place in the city of Lux, a man-made underground city that has crumbled after years of neglect and lack of repairs. Citizens of Lux have come to refer to their home as simply "The City" and treat it as though it has a mind and will of its own. Three major factions battle to control Lux: Organo, a group of "professionals" who collaborate with the criminal underworld that controls Texhnolyze (prosthetics), the Salvation Union, a populist group that seeks to disrupt Organo's business, and Racan, a collection of young individuals with Texhnolyzes that use their abilities for personal gain. Ichise was once an orphan who has made a place for himself in Lux as a prize fighter. One day, a fight promoter grows angry with him and the altercation that follows results in Ichise losing an arm and a leg. Before death can take him, Ichise is found by the scientist Eriko Kamata, who uses him as a test subject for her newly designed Texhnolyze. With these powerful new limbs at his disposal, Ichise begins to work for Oonishi, the leader of Organo. He soon meets a mysterious young girl, Ran, who has the power to see possible futures. Together, they soon realize that Lux is on the brink of war and collapse, and that they may be the only ones who can save The City.

The Four Cardinal Heroes are a group of ordinary men from modern-day Japan summoned to the kingdom of Melromarc to become its saviors. Melromarc is a country plagued by the Waves of Catastrophe that have repeatedly ravaged the land and brought disaster to its citizens for centuries. The four heroes are respectively bestowed a sword, spear, bow, and shield to vanquish these Waves. Naofumi Iwatani, an otaku, becomes cursed with the fate of being the "Shield Hero." Armed with only a measly shield, Naofumi is belittled and ridiculed by his fellow heroes and the kingdom's people due to his weak offensive capabilities and lackluster personality. When the heroes are provided with resources and comrades to train with, Naofumi sets out with the only person willing to train alongside him, Malty Melromarc. He is soon betrayed by her, however, and becomes falsely accused of taking advantage of her. Naofumi then becomes heavily discriminated against and hated by the people of Melromarc for something he didn't do. With a raging storm of hurt and mistrust in his heart, Naofumi begins his journey of strengthening himself and his reputation. Further along however, the difficulty of being on his own sets in, so Naofumi buys a demi-human slave on the verge of death named Raphtalia to accompany him on his travels. As the Waves approach the kingdom, Naofumi and Raphtalia must fight for the survival of the kingdom and protect the people of Melromarc from their ill-fated future.