Haruka Nanase and Makoto Tachibana have started middle school and must adjust to the changes that come along with growing up. While Makoto fits in with his classmates and remains positive about swimming, Haruka struggles to befriend others or join his school's swim club, as his previous issues with swimming trouble him. Distancing himself from his lively classmates and the swimming club, he has difficulty deciding which club to join instead. The rest of his classmates, including Makoto, are also hesitant as to which clubs to participate in. After an argument leads them to join the swimming club anyway, the boys strive to hone their skills, harmonize their swimming styles, and refine their conflicting feelings toward swimming and each other. As determination and talent run high, Haruka and Makoto—along with their classmates—discover themselves and improve their talents during their starting days.

Human civilization no longer revolves around fire, but is instead now driven by fear of it. Repeated wars have changed human biology, and people now spontaneously combust when they get close to natural flame. However, a new source of energy prevents society from complete collapse: a stone-shaped material used to produce light and steam lies within the bodies of monsters that infest numerous forests. Those tasked with collecting this precious resource are called fire hunters. Touko, a young village girl, is saved from a forest monster by a fire hunter who perishes during his heroic action. After the hunter's dog, Kanata, heals from his own injury, the girl's family sends her to the capital in order to return Kanata and the hunter's fire sickle to his relatives. Elsewhere, the fire hunter's son, Koushi, and his sister are adopted by a wealthy family. Koushi learns some troubling facts related to the country's ruling royal family. He conducts secret research on a special fire stone found by his late father, kickstarting a race against time between the country's leaders and those trying to save mankind from its ultimate demise.

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. (Source: Wikipedia)

While searching through his grandfather's attic, Hikaru Shindou stumbles upon an old go board. Touching it, he is greeted by a mysterious voice, and soon after falls unconscious. When he regains his senses, he discovers that the voice is still present and belongs to Fujiwara no Sai, the spirit of an ancient go expert. A go instructor for the Japanese Emperor in the Heian Era, Sai's passion for the game transcends time and space, allowing him to continue playing his beloved game as a ghostly entity. Sai's ultimate goal is to master a divine go technique that no player has achieved so far, and he seeks to accomplish this by playing the board game through Hikaru. Despite having no interest in board games, Hikaru reluctantly agrees to play, executing moves as instructed by Sai. However, when he encounters the young go prodigy Akira Touya, a passion for the game is slowly ignited within him. Inspired by his newfound rival, Hikaru's journey into the world of go is just beginning.