Arita Haruyuki. A young boy whose chubby appearance and shy disposition makes him a constant target for school bullying. Ashamed of his miserable life, Haruyuki can only cope by indulging in virtual games. That all changes when Kuroyukihime, the most popular girl in school, introduces him to a mysterious program called Brain Burst.
Haruyuki, now a Burst-Linker, suddenly finds himself thrown into a deadly match against a vicious biker named Ash Roller. Haruyuki is unable to grasp the situation and is quickly defeated. He later finds out from Kuroyukihime that the Brain Burst program is a fighting game designed to win points necessary to accelerate. In order to regain the points he lost, Haruyuki vows for a rematch.
A Duel Avatar called Cyan Pile is seeking to challenge Kuroyukihime in battle within Accel World. Haruyuki is later asked by Kuroyukihime to help her uncover the identity of Cyan Pile, and he is shocked to learn that one of the potential suspects is his childhood friend Chiyuri.
Haruyuki suspects that Cyan Pile is challenging Kuroyukihime within Accel World via access through Chiyuri's neuro-linker. But when he tries to share his theory with Kuroyukihime, she walks off without saying a word, upset over the fact that Haruyuki engaged a direct link with Chiyuri.
The identity of Cyan Pile is revealed to be one of Haruyuki's closest peers, who has been consumed by the power to accelerate. To protect Kuroyukihime, Haruyuki challenges his former friend to a duel as Silver Crow.
The battle between Silver Crow and Cyan Pile ends with Silver Crow's victory. Having reconciled with Takumu, Haruyuki now focuses on training to level up in Accel World. Everything seems to be going smoothly for Haruyuki until he makes one small mistake...a costly mistake that could mean losing all of his Burst Points.
Haruyuki hires a bouncer known as Aqua Current to guard him until he can regain his lost Burst Points. Meanwhile, Kuroyukihime challenges Takumu to a Brain Burst match.
Haruyuki comes home one day to find a cute young girl greeting him with a smile. Claiming to be a distant relative, the girl then tells Haruyuki that she will be staying at his place for a few days.
Haruyuki's little guest is revealed as Scarlet Rain, a.k.a. the Red King. The Red King explains to the members of Nega Nebulous that she requires the assistance of Silver Crow's unique ability in order to destroy a certain being.
The unexpected drama of letting Kuroyukihime and Niko spend the night at his place has left Haruyuki feeling very tired. The next day, the team begins their mission to track and hunt down Chrome Disaster.
During their hunt for Chrome Disaster, the Nega Nebulous is ambushed by the Yellow Legion led by Yellow Radio, a.k.a. the Yellow King. Yellow Radio takes advantage of the non-aggression pact shared between the other kings to justify his act of revenge against Scarlet Rain, and even manages to neutralize Black Lotus by reminding her of the past sin she has committed.
The battle between Black Lotus and Yellow Radio is halted by the sudden appearance of Chrome Disaster. Silver Crow is wracked with fear as he witnesses the monstrous power of his target. In order to restore her knight's confidence, Black Lotus engages Chrome Disaster herself, reminding Silver Crow what it means to be a Burst Linker.
It is the start of a new school year. Haruyuki and Takumu reluctantly agree to install the Brain Burst program into Chiyuri, who hopes that this will bring them closer together, like old times. After the program is successfully installed, Haruyuki and Takumu are surprised to learn that Chiyuri's Dual Avatar possesses a very rare and unique ability.
Takumu loses a kendo match to a new student named Nomi, who appears to be using the power to accelerate. But the matching list does not show any new Duel Avatars appearing in the area. In order to confirm their suspicions, Haruyuki and Takumu start investigating to find any evidence that would point to Nomi being a Burst Linker.
Haruyuki rebuffs Nomi's threat and challenges him to a duel, only to lose in an unexpected way. To make matters worse, Haruyuki's defeat causes him to lose his greatest ability.
Ash Roller takes Silver Crow to meet his master Sky Raker, previously known as the Burst Linker who came closest to flying in Accel World. Sky Raker explains the "Incarnate System," which allows Burst Linkers access to their hidden powers. She also goes into how that same power led to her own downfall.
Haruyuki receives a call from Kuroyukihime, who is away on a school trip. Touched by her kind words, Haruyuki vows to settle the score with Dusk Taker on his own. Meanwhile, Takumu learns of what happened to his friends and decides to challenge Nomi to a duel.
During her stay in Okinawa, Kuroyukihime is challenged to a Brain Burst match by two girls named Ruka and Mana. Kuroyukihime easily wins the match, but learns that the girls were actually testing her to see if she was powerful enough to help solve their problem. Although suspicious of their true intentions, Kuroyukihime nonetheless agrees to meet the girls in person to hear what they have to say.
Ruka and Mana introduce Kuroyukihime to their master, Crimson King, who turns out to be an old acquaintance of Kuroyukihime's. According to Crimson King, a very powerful Enemy is preventing them from hunting down regular Enemy units within Okinawa's field with no limits. To make matters even worse, that same Enemy is under the control of a Burst Linker calling himself Sulfur Pot, who comes to attack Kuroyukihime and the others.
Silver Crow and Cyan Pile's combined attack severely weakens Dusk Taker. But the two are shocked when they see Chiyuri enter the battlefield as Lime Bell and heal Dusk Taker. Fully recovered, Dusk Taker mutilates Cyan Pile, leaving Silver Crow on his own.
Haruyuki asks Niko to help train Takumu in obtaining the "Incarnation." But Niko explains that in order to obtain it, one must first confront one's personal weakness, the same weakness that influenced the appearance of the person's Dual Avatar.
In Akihabara, Haruyuki and Pard hear the name of a Burst Linker called Rust Jigsaw who doesn't show up on the matching list. Believing he may hold a clue to uncover Dusk Taker's secret, Haruyuki and Pard challenge Rust Jigsaw to a duel and confirm their suspicions. Elsewhere, Lime Bell is making her official debut as a Burst Linker in Accel World.
Haruyuki and Takumu set out for their final showdown with Nomi. Chiyuri wishes to join them, and they agree to let her come along. But a sudden ambush by an unknown Burst Linker traps Silver Crow, leaving Cyan Pile to take on Dusk Taker alone.
Silver Crow is determined to settle his score with Dusk Taker once and for all. After a fierce battle in midair, Silver Crow delivers his "Incarnation" attack on Dusk Taker, only for Lime Bell to use her Citron Call to "heal" him once again.