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.

Haruyuki, now a Burst-Linker, suddenly finds himself thrown into a deadly match against a vicious biker named Ash Roller.

A Duel Avatar called Cyan Pile is seeking to challenge Kuroyukihime in battle within Accel World.

Haruyuki suspects that Cyan Pile is challenging Kuroyukihime within Accel World via access through Chiyuri's neuro-linker.

The identity of Cyan Pile is revealed to be one of Haruyuki's closest peers, who has been consumed by the power to accelerate.

After Haru and Takumu reveal everything to Chiyuri, who doesn't take it too well, the two begin training to work as a tag team. Haru earns enough points to upgrade to level 2, though in his haste, he upgrades too early and is left with a low amount of Burst Points as a result.

As Kuroyukihime suddenly challenges Takumu to a match, confronting him about his intention to quit kendo and eventually uninstall Brain Burst. Current agrees to join Haru until he can get his points up to 50 and enters a tag match with him.

As Kuroyukihime's team attempts to claim more territories, Haru finds his tactics are becoming easily read by his opponents. He returns home to be greeted by Tomoko Saito, who is allegedly his second cousin who is staying with him whilst her parents are away.

After discussing with Takumu, Kuroyukihime agrees to meet up with Tomoko, whose real name is Yuziko Kozuki. Yuziko explains how she wishes to borrow Haru's power of flight to destroy the Armor of Catastrophe.

After having another misunderstanding cleared up for her, Chiyu expresses and interest in becoming a Burst Linker. As Kuroyukihime explains how the ability to give someone a copy of Brain Burst and become their guardian can only be used once, Haru becomes intrigued as to who her guardian was.

Both Haru and Yuniko realize that Yellow Radio was the one responsible for the fifth Chrome Disaster, using a loophole in the non-aggression treaty as an excuse to eliminate her and reach Level 10. He then takes out Kuroyukihime and starts bombarding Haru and Yuniko.

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.

Chiyu gets Takumu to install Brain Burst for her and becomes a Burst Linker, gaining the Duel Avatar, Lime Bell. Kuroyukihime during assembly, believes there may be another Burst Linker among the new students.

As Haru, Takumu and Chiyu discuss what exactly Seiji is, Takumu deduces the ability Seiji used was Physical Burst, which accelerates the user's consciousness, allowing them to react quicker. As Kuroyukihime heads off on her school trip, Haru and Takumu decide to investigate Seiji in an attempt to get some proof of him being a Burst Linker.

Although Haru seemingly dominates the match to begin with, Seiji manages to trap him and use his Demonic Command ability to steal Haru's flight ability. As Haru tries to keep what happened a secret from Takumu, their friendship is put under pressure.

Raker explains to Haru that although he had lost his wings, he may be able to fly if he learns to use the 'incarnate system', which allows avatars to use certain powers through their will power alone. Later that night, Raker explains how her jumping ability led to her obsession with flying.

As Haru contemplates how to go about facing Seiji, he receives a video call from Kuroyukihime, who mentions giving some information about Seiji to Takumu. During gym that day, Takumu challenges Seiji to a battle.

Over in Okinawa, Kuroyukihime is on her school trip with her friend Megumi. They are approached by two local Burst Linkers; Ruka Asagi and Mana Itosu, who ask to help their master fight against a monster that is plaguing their Accel community.

Ruka and Mana introduce Kuroyukihime to their master, Crimson King, an old acquaintance of Kuroyukihime's. According to Crimson King, a powerful Enemy is preventing them from hunting down regular Enemy units within Okinawa's field with no limits.

Having been fully healed by Chiyu, Nomi makes short work of Takumu and defeats him in horrific fashion. As Haru is overcome with anger, he is overcome by a dark power urging him to destroy Nomi, displaying a similar power to Dusk Taker.

As they make their way to meet up with Yuniko, Haru explains to Takumu how Seiji had set him and Chiyo up. After hearing about their situation, Yuniko agrees to teach Haru and Takumu about the incarnate system.

Leopard decides to enter herself and Haru into a tournament to lure out Jigsaw, she also explains to Haru how overusing the incarnate system can bring him closer to darkness.

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.