The journey of Satoshi and his friends through the Kalos region continues! After Satoshi obtains his seventh gym badge, the group is moving toward the next town when Eureka discovers a mysterious Pokemon resting in her pochette. Soon given the name Puni-chan, it is one that even Satoshi and Serena's new Pokemon Zukan cannot identify. However, it quickly becomes apparent that Puni-chan is the target of a mysterious group clad in bright red suits known as Team Flare, aiming to capture the new Pokemon to further their agenda. But when Satoshi and the gang realize that the enigmatic organization has no intention of treating Puni-chan with any decency, they take a stand in opposition to Team Flare's plans, daring to fight back. With Gojika's predictions looming above them, Satoshi aims for his final gym badge while Serena contests for her last Princess Key in order to be able to compete at the TriPokalon Master Class. But as Team Flare begins to move in search of the mysterious Z, the stories of Pokemon XY and Pokemon XY: Mega Evolution cross paths as Satoshi and his friends, along with Team Rocket, get caught up in a scheme that could put Kalos in great danger. [Written by MAL Rewrite]

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.

Youko Nakajima has only ever wanted to be normal. She does what she is asked, gets good grades, is the class president, and even helps her classmates whenever she can—but because of her red hair, she has never fit in. With her pushover attitude, Youko lets classmates take advantage of her, so she has nobody she can really call a friend. But on an otherwise ordinary day, a man who claims to be from another world barges into Youko's classroom and bows before her. This elegant blond-haired man, Keiki, claims that Youko is his master and belongs on the throne of his kingdom. However, their first meeting is cut short as Keiki has been followed by otherworldly beasts called youma. He is able to escape with Youko into his own realm, but two other classmates—Ikuya Asano and Yuka Sugimoto—are caught up in the madness as well. Unfortunately, their troubles have only just begun, as the youma attack leaves them separated from Keiki. Alone in this strange new land, these ordinary students must learn to fend for themselves or die.

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.