Beginning his first year of high school, all Matsuboshi Raidou wants is to make friends—starting with the cute, tiny, and soft-spoken Reina Aharen, who sits right next to him in class. Unbeknownst to Raidou, Reina shares the same sentiment, but she has a problem. Awkward and timid, Reina is incapable of determining how chummy she has to be when approaching a person. Due to Reina's complete inability to gauge personal space, the two struggle to spark their unlikely friendship, as even the simplest tasks like talking seem impossible for them. But despite the countless yet pointless challenges that hinder the pair, the overly imaginative Raidou will do whatever it takes to befriend the indecipherable Reina.

Some time after the events involving Burst Linker Dusk Taker, Kuroyukihime recalls recruiting Haruyuki Arita to the Brain Burst program—an application that allows players to accelerate their cognitive functions until time seems to stop. Since his arrival, Haruyuki has risen to fame among the other Burst Linkers and has been helping Kuroyukihime achieve her goal of reaching the highest level in the game. During a territorial battle with their legion, Nega Nebulus, Haruyuki and his friends are kicked out of the program after a destructive storm in-game. All over Tokyo, security cameras are malfunctioning, which Kuroyukihime deduces is related to the Brain Burst glitch. Determined to fix the problem, Nega Nebulus must recruit the other legions to find the source of the issue and restore the acceleration ability.

Haruyuki Arita is an overweight, bullied middle schooler who finds solace in playing online games. But his life takes a drastic turn one day, when he finds that all his high scores have been topped by Kuroyukihime, the popular vice president of the student council. She then invites him to the student lounge and introduces him to Brain Burst, a program which allows the users to accelerate their brain waves to the point where time seems to stop. Brain Burst also functions as an augmented reality fighting game, and in order to get more points to accelerate, users must win duels against other players. However, if a user loses all their points, they will also lose access to Brain Burst forever. Kuroyukihime explains that she chose to show Haruyuki the program because she needs his help. She wants to meet the creator of Brain Burst and uncover the reason of why it was created, but that's easier said than done; to do so, she must defeat the Six Kings of Pure Color, powerful faction leaders within the game, and reach level 10, the highest level attainable. After the girl helps Haruyuki overcome the bullies that torment him, he vows to help her realize her goal, and so begins the duo's fight to reach the top.

Individuals who can materialize weapons from their soul are called Blazers, and they attend Kouryou Academy High School in order to harness their abilities. Each student is required to partner with another, in the hopes that one day, the pair can attain the power of Absolute Duo. Tooru Kokonoe hopes to attend this academy in order to gain power after his sister and friends were slain by a mysterious man. However, at the opening ceremony, he is forced to duel against the person sitting next to him, with the loser being expelled. As Tooru prepares to give the match his all, it is not a weapon that manifests from his soul, but a shield, an irregularity which catches the attention of a foreign student named Julie Sigtuna.