Seirin High School's quarterfinal opponent in the Winter Cup is the highly defensive Yousen High School. Much of their Shield of Aegis defense is thanks to Atsushi Murasakibara, one of Tetsuya Kuroko's former Generation of Miracles teammates, and Tatsuya Himuro, a skilled player who has a history with Taiga Kagami. Unable to settle their previous score, Kagami and Himuro resolve to use this high-stakes match to determine the superior player. At the same time, Kuroko's past gripes with his former teammate make the atmosphere on the court even more intense. If they manage to make it past Yousen, Seirin's old rivals at Kaijou High await them in the semifinals, including another of Kuroko's former teammates, Ryouta Kise. Figuring out how to dismantle Kise's Perfect Copy will be the key to Seirin's victory, but this may be a tall order when they realize that Kaijou's star has learned to copy the other Miracles' playstyles.

It is Tetsuya Kuroko's birthday. In celebration, Satsuki Momoi has invited the other members of the Generation of Miracles to play basketball together and rekindle the memories from their nostalgic middle school days. Meanwhile, Taiga Kagami and his fellow teammates of Seirin High are doing their best to prepare for Kuroko's birthday party. Sometimes, the best gift one can receive is not a material one but, rather, the feeling of having fun with everyone!

High school student Ibuki Keita has been haunted by misfortune for as long as he can remember. For no apparent reason, everyone around him dies tragically. Ultimately, he refuses to become too close to anyone, even his childhood friend Akane. This leaves Keita alone in a life full of misery and disgrace. While eating at his favorite ramen shop one evening, Keita meets a strange young girl named Kuro. Possessing abilities that surpass that of a normal human being, Kuro classifies herself as a Mototsumitama. She explains to Keita about Terra, a life-energy force split between three identical looking people; a global phenomenon dubbed the Doppeliner System. As a Mototsumitama, Kuro guards the Coexistence Equilibrium, the beings that protect the flow of Terra around the world. Keita refuses to believe her story, until he is caught up in the crossfire of this hidden world. On the verge of death, he makes a contract with Kuro, unbeknownst to its true meaning. Now he is bound to Kuro, and must be with her at all times. Could Keita's misfortune possibly get any greater?

During the dawn of the 21st century, the United Nations Kurobe Research Institute was established in Japan to investigate an ancient artifact, which was discovered during the construction of the Kurobe Dam. Scientists from around the world have gathered in the facility to study the object, while their children enjoy their everyday lives attending Mt. Tate International Senior High School. Yukina Shirahane, a reserved high school girl, is the daughter of the facility's head scientist. While visiting her mother at the facility, Yukina manages to solve part of the artifact's puzzle. To her surprise, what appears before her is Kennosuke Tokisada Ouma, a young samurai from the Sengoku era. As a threat approaches from outer space, Yukina, along with Kennosuke, finds herself defending Earth against the invading forces. Along the way, she discovers the mystery behind Kennosuke and the reason he is determined to protect her.