After the decision to serialize Moritaka and Akito has been made, they are introduced to Miura, their new manager. At first, the two thought it was a joke, but Hattori gives them a pep talk before leaving. While Miura doesn't seem like a bad person, he is given to rudeness and seems to be worried about the duo's future. In addition, the duo are given 3 assistants to work on their manuscript, and with the assistance of Ogawa, an experienced assistant, their work progresses well. At the start of the new year, Moritaka and Akito both attend Shonen Jack's New Year Party. There, they meet Hiramaru Kazuya, said to be a genius of a whole different level from Eiji.
The story takes place in Tokyo in 2039. After the outbreak of the unidentified virus "Lost Christmas" in 2029, Japan has been under the control of a multinational organization called GHQ. Ouma Shu is a 17-year-old boy who has a psychic power in his right hand. He can use the power "Ability of King" to extract tools or weapons from his friends. He has been avoiding making trouble for others but his life changes when he meets a girl named Yuzuriha Inori, a member of a resistance guerrilla group called "Undertaker", whose members pilot mecha weapons to fight against the government.
Middle school 2nd year, Amano Yukiteru, is a boy who has problem making friends. He thinks of himself as a bystander and will always write down everything he sees in a cell phone diary. Tormented by solitude, Yukiteru began to imagine things like a friend called Deus Ex Machina who is apparently the Lord of Time & Space. Seeing Yukiteru's miserable state, Deus gives him a new ability. His diary will now record events that will happen in the near future. Yukiteru is then forced to participate in a game which the winner will become Deus's successor.
Continuing from the events of the last series (Shakugan no Shana II), both Shana and Kazumi stand at their respective locations waiting for Yuji to meet with one of them, only to discover that Yuji has disappeared, with not even the slightest evidence of his existence left behind. All is not lost however, as the letters the two of them sent to him still give hope of Yuji's continued existence. As Shana and company search for answers on Yuji's whereabouts, they soon find the truth staring back at them when Yuji reappears in front of them as the leader of Bal Masqué. Left with little choice, Shana must now confront her most unlikely adversary on the battlefield in her toughest challenge yet.
Second season. Set in a family restaurant in Hokkaido, the northern prefecture of Japan, 16 year old high school student Takanashi Souta works part-time along with his strange co-workers: Taneshima Poplar, a high school girl who's a year older than Souta and easily mistaken for an elementary/middle schooler, and Shirafuji Kyouko, the 28-year old store manager who doesn't bother to do any work at all.
