Haruyuki Arita receives an e-mail from Araya, one of the students who has been bullying him, demanding that he buys him and his buddies food for lunch. Afterwards, he hides in the restroom where he links into the virtual world as a pig. As he walks towards the squash court, he sees the student council vice-president Kuroyukihime being admired by other students, while she notices him. He sets a new high score in squash and when he is about to start another game, Chiyuri Kurashima finds him and forces him to link out. Chiyuri advises Haruyuki to send the e-mails to the faculty and asks him to have lunch together, but Haruyuki refuses and runs away. Returning to the squash court, he sees that his high score is surpassed and Kuroyukihime appears before him asking him meet her during lunch the next day, promising to change his reality. On the next day, Kuroyukihime introduces Haruyuki to the Brain Burst program that allows users to "accelerate" their brain waves to make time appear to stand still. Araya, having been provoked by Kuroyukihime, throws a punch at Haruyuki, but before the punch lands the burst link is activated. While in accelerated mode, Kuroyukihime advises Haruyuki to let the punch land and to throw himself at her so that Araya would be caught on the security camera in front of several witnesses, which Haruyuki agrees to do. After exiting burst link mode, Haruyuki does exactly that and Araya is detained by security. On the way home from school, Haruyuki and Chiyuri meet up with Takumu Mayuzumi and Haruyuki runs home alone after believing that Takumu was informed about what happened during lunch. On the next day, Haruyuki connects to the Global Net to check that he has his lunch money against Kuroyukihime's orders and on his way to school, he is transported into a war-torn world where he transforms into Silver Crow and is challenged by Ash Roller to a duel.
A clueless Haruyuki is easily beaten by Ash Roller in the duel. During lunch, Kuroyukihime and Haruyuki enter the accelerated world and Kuroyukihime explains to Haruyuki that in order to continue accelerating that he must fight and defeat other Brain Burst avatars. She also points out that the avatar is created based on the thoughts of the user, which in Haruyuki's case it is his inferiority complex. When Kuroyukihime offers to let Haruyuki return to his normal life, Haruyuki declines stating that he owes her for changing his life. Having agreed to further his friendship with Kuroyukihime, she orders him to learn how to fight. After linking out, Kuroyukihime explains to the students in the dining room that she asked Haruyuki to go out on a date and he rejected it, much to everybody's surprise. After school, Haruyuki challenges Ash Roller to a rematch and forms a strategy using the information given by Kuroyukihime. Haruyuki starts off with a surprise attack with the intent to stall until time ran out, but Ash Roller obtained the ability to climb walls on his motorcycle making that strategy impossible. A desperate Haruyuki attempts his killer move, the headbutt, but instead he is rolled over by the motorcycle. Haruyuki then figures out Ash Roller's weakness and lifts the rear wheel off the ground to immobilize Ash Roller since the motorcycle is a rear wheel drive model from the 20th century. Haruyuki headbutts Ash Roller at close range to win the duel. After exiting the accelerated world, Chiyuri sees Haruyuki and Kuroyukihime together and is mad at Kuroyukihime for getting Haruyuki hurt.
Kuroyukihime tells Chiyuri that she is dating Haru and drags him to a cafe. While there, Kuroyukihime explains her dilemma to Haru. Brain Burst was anonymously created seven years ago which allows acceleration only to those who were born with the Neurolinker. Therefore, all Burst Linkers are children age 15 and younger, allowing its existence to be concealed from the public. Kuroyukihime wants to meet the creator to learn the purpose of the program. To do that, she needs to reach level 10, which requires five wins over level 9 Burst Linkers and one defeat results in the permanent uninstallation of Brain Burst. Two years ago, Kuroyukihime was one of the Kings of Pure Color, a group of level 9 Burst Linkers that agreed to not fight each other, but she did not agree to the treaty and beheaded the Red King, causing her to be branded a traitor and leading her to seal away Black Lotus. Since then, she has stayed offline, only logging on to the school's local net with a dummy avatar. Recently, she was challenged to a duel by a Burst Linker named Cyan Pile, which could lead to her identity as Black Lotus being exposed. Thus, she must find Cyan Pile's identity. She suspects Chiyuri, which is why she provoked her, although Haru doubts it knowing that Chiyuri is bad at games. Haru begins the investigation by going to Chiyuri's home under the pretense of apologizing for lunch the other day. The two link up with each other with an extremely short cable and reconcile with each other, with Chiyuri letting Haru know that Takumu was not told about the bullying. During the conversation, Haru discovers that while Chiyuri is not Cyan Pile, there is a back door connection that could lead to finding its identity.
As Haru chooses not to meddle with the backdoor to avoid detection, he finds Kuroyukihime starting to act strangely around him when he mentions how close he had gotten to Chiyuri. When Haru is interviewed by a pair of gossip club students, they hint that Kuroyukihime legitimately likes him, which he refuses to believe. As Kuroyukihime and Haru walk together that day, Haru resides himself to just being a pawn, prompting a slap from her. Just then, an out of control car heads straight towards Haru and Kuroyukihime, prompting them to go into the Accel World. As Kuroyukihime confesses to Haru that she is love with him, she uses a powerful move which causes her Brain Burst to drop to lower levels, allowing her to manipulate her body in the Accel World to push Haru out of the way of the car, leading to only her being hit. As Kuroyukihime is taken into intensive care, Haru comes to realise that if she was to be attacked by a Burst Linker now, she would be completely vulnerable, and so chooses to stay the night. As the morning comes, Haru spots Takumu coming into the hospital and comes to realise that he is the true Cyan Pile. With just a split second to act, Haru rushes to challenge Takumu to a Brain Burst match before he can challenge Kuroyukihime.
As Haru learns just how horrible of a person Takumu is, he flees from Cyan Pile's attacks, losing one of Silver Crow's arms in the process. Haru initially gets the advantage thanks to his speed, but is soon hit by Takumu's special attack and loses a foot as well. As Takumu vents his anger on how Chiyuri is always thinking about Haru, he hits him with a powerful attack that leaves him with a fraction of health. Haru finds himself in a basement where he finds Kuroyukihime's sleeping avatar, whose beating heart reminds him how strength isn't always about winning. Just then, Haru gains a new power in the form of wings, making him the first flying Brain Burst avatar and allowing him to fly back up and overcome Takumu's attack. In leau of defeating Takumu, causing him to lose all his points and his Burst Linker status, Haru asks him to become one of his allies and start over. Afterwards, Kuroyukihime appears and decides to reveal her avatar's true form, Black Lotus, announcing her goals to the spectators. Everyone was shocked to see that Black Lotus is still alive. Later, as Haru visits Kuroyukihime in hospital, she asks him to call her by her first name.
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. Takumu offers to share some of his points with Haru, but he declines, saying it would take all the honor out of fighting. Afterwards, the two go over to Chiyuri's where they eat ice cream together and explain to Chiyuri about Brain Burst. It is here where Takumu gets the idea to have Haru hire a bodyguard known as Aqua Current to protect him until he gets his points up. As Haru goes through the procedures to hire Aqua, he inadvertantly discovers it is actually a girl. As Haru discusses things with Aqua, Takumu meets with Kuroyukihime, who activates her Burst Link.
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 teaches Takumu to stop feeling guilty and trust his friends more, Haru and Current manage to work together to win their match, getting his points back up to 54. Just then, Current challenges Haru to a match with the intention of taking all his points. As Haru shows he is still willing to believe in her and doesn't fight back, she reveals she was lying, telling him to treasure his friends before erasing his memory of her. The next day, Takumu transfers into Haru and Chiyuri's school wearing glasses, hoping to see the true world with his own eyes.
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. Haru soon deduces that she is in fact a Burst Linker known as Scarlet Rain, revealed by Kuroyukihime to be the Red King. Following a mishap in the bathroom, Tomoko challenges him to a Brain Burst match, proving to be too powerful for him. As Tomoko wins the match, she requests a real life meeting with Kuroyukihime. As Haru discusses the matter with Kuroyukihime, she reveals she had a thing for the previous Red King, Red Rider, who she had beheaded when she betrayed the other Level 9s.
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, an external item that turns Burst Linkers into Chrome Disasters which Kuroyukihime had thought was long destroyed. After Kuroyukihime explains to everyone about how she had fought the last Burst Linker who was possessed by the armor, Yuziko reveals that the current Chrome Disaster is from her own legion, explaining how she needs Haru's flight to get close enough to use an ability to instantly defeat him. After agreeing to the terms, Kuroyukihime becomes jealous of Yuziko and decides to spend the night at Haru's home.
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. When asked, Kuroyukihime only replies that it is someone who betrayed her trust, also explaining how a relationship between guardian and protegé is different from others. Later that day, Haru, Kuroyukihime, Takumu and Yuniko gather together and enter the Unlimited Accel World to search for Chrome Disaster. As they make their ways towards them, they are ambushed by a group of Burst Linkers led by the Yellow King, Yellow Radio.
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 by displaying a recording of herself beheading Red Rider, the first Red King, demoralizing her enough that she faints. Haru, Yuniko and Takumu are then forced to endure the onslaught from the Yellow Legion. During the battle, Takumu sacrifices himself to buy the others time. As the Yellow Legion starts to overwhelm them, Haru urges Kuroyukihime to wake up and she does. Kuroyukihime does battle with Yellow Radio and just as they charge up their killer moves, Yellow Radio is impaled by Chrome Disaster.
As Yellow Radio retreats, Kuroyukihime fights off against Chrome Disaster but is suddenly attacked by Yuniko, claiming that they aren't allies. Despite Yuniko's supposed betrayal, Kuroyukihime assures Haru that she is just being stubborn and asks him to help save their friend. As Chrome Disaster attempts to escape the Accel World, Haru manages to use his gadgets against him and defeat him, allowing Yuniko to administer the Judgement Blow to remove him from Brain Burst. Afterwards, Yuniko laments how, after Cherry Rook had introduced her to Brain Burst, she became ignorant to his problems after becoming level 9. After checking the Armor of Destruction was completely destroyed, Haru hears a voice a strange voice, though passes it off as his imagination and logs out, unaware that something has lynched onto his back. Later, Yuniko once again moves into Haru's place, explaining the reason Cherry Rook was so desperate to become stronger was because he was about to move, but she managed to assure him there are more ways than Brain Burst to stay in touch.
Chiyu gets Takumu to install Brain Burst for her and becomes a Burst Linker, gaining the Duel Avatar, Lime Bell. The next day as a new school year comes and Haru, Chiyu and Takumu are in the same class, Haru notices some odd behaviour from Kuroyukihime during assembly, believing there may be another Burst Linker among the new students. Whilst checking out to see if any new Burst Linkers are around, with no such luck, Haru and Taku help get a grasp of Lime Bell's abilities, deducing that she's a healer type. As Haru reports this to Kuroyukihime, she explains that she is likely to be scouted, as the only other healer in Brain Burst is one of the Six Kings. Kuroyukihime then reveals she is going on a school trip to Okinawa, tasking Haru and the others with defending her territory. Later, as Takumu participates in a kendo tournament, Haru discovers that his opponent, a freshman named Nomi, is using some sort of Burst power, but doesn't appear to be a Burst Linker upon inspection.
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. However, Seiji throws Haru off and uses a visual mask to lead him to the girls' shower room, where Chiyu is forced to hide him. The next day, Haru is confronted by Seiji, who wants to blackmail him into giving him more Burst Points. Chiyu stands up for Haru, but Seiji once again gains the upper hand when he lets a hidden camera in the shower room be found. As Haru attempts to fight back, Seiji overwhelms him and forces him into a Brain Burst duel, where he reveals his avatar, Dusk Taker.
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, leaving Haru devastated as he boasts that he won't return them until he graduates. Seiji then proceeds to win the match and takes Haru's point, reminding both him and Chiyu about the power he holds over them, forcing them to keep it a secret from Takumu and Kuroyukihime. As Haru tries to keep what happened a secret from Takumu, their friendship is put under pressure. As Haru falls into depression, uncertain about what to do, he enters another match with Ash Roller but ends up feeling useless without his wings. Taking pity on his lack of motivation, Ash takes Haru to a green place in the Accel World to meet his guardian, Sky Raker.
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 an obsession to want to fly, leading her to ask Kuroyukihime to cut off her legs. As the training begins, Raker first tasks Haru with climbing up the large tower where Raker's abode is, which proves difficult when the changing field turns the tower into metal. However, Haru soon starts to use his will power to learn how to pierce into the metal, also taking into consideration what Kuroyukihime told him about his speed. On the 7th day, Haru finally puts what he had learnt to practise and reaches the top of the tower. The next day, Raker meets up with Haru in real life to give him her armament, Gale Thruster, with Haru promising to regain his flight using his own power so he can return it back to her some day.
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, revealing he knew about Haru's ability being stolen. Although Takumu initially gains the upper hand, Seiji uses the incarnate system to give himself powerful arms and overwhelm Takumu. Haru manages to trick Seiji into switching to Battle Royale mode so he can fight against him instead, managing to cut off one of his arms with his own icarnation attack. As Seiji activates Haru's wings and some pyro equipment, Haru equips the Gale Thruster he received from Raker, allowing him to take to the skies and face Seiji head on and manages to beat him with assistance from Takumu. However, before Haru can finish him, Chiyu appears and heals Seiji.
Over in Okinawa, Kuroyukihime is on her school trip with her friend Megumi. As the two go souvenir shopping for eachother, Kuroyukihime is approached by two local Burst Linkers, Ruka Asagi and Mana Itosu, who ask her to help their master fight against a monster that is plaguing their Accel community. The discussion causes Kuroyukihime to lose track of time and forget to buy Megumi a present, which upsets her. Kuroyukihime apologises to Megumi by telling her that, since discovering Brain Burst seven years ago, she is the one who kept her tied to the real world. The next day, Kuroyukihime enters the Accel World with Ruka and Mana to meet up with their master, who turns out to be an old acquaintance of Kuroyukihime's.
Kuroyukihime is reunited with Crimson Kingbolt, aka "Crikin", a Burst Linker who moved from Tokyo to Okinawa after his parents divorced. Just then, they are surprised by the mysterious threat, revealed to be a Burst Linker named Sulfur Pot, who has the power to tame "enemies". When it is mentioned that Sulfur Pot doesn't appear on the challenge list, Kuroyukihime realizes that he's from Tokyo, using a backdoor program to dive into Okinawa. As they fight, in the real world, Megumi finds Kuroyukihime, Ruka and Mana's bodies slumbering while linked up. As she reached to disconnect Kuroyukihime, she sees a vision of her younger self, urging her not to do it. Megumi then spots a spare cable and plugs into Accel World. Her avatar, Orchid Oracle, changes the landscape to an ocean, giving Kuroyukihime and her allies an advantage against Sulfur Pot. After severing control of his mount, the enemy then devours him. Kingbolt then gives Kuroyukihime the enhanced armament that Sulfur Pot used to control the enemy, figuring she may use it one day. As Kuroyukihime departs Okinawa, Ruka and Mana see her off. Kingbolt then sends her message informing her that the trail on Sulfur Pot has gone cold. Kuroyukihime can then only wonder about the mysterious faction Sulfur Pot belongs to.
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, though the timer ends the battle before it can escalate any further. Upon returning to the real world, Haru and Takumu confront Chiyu, who claims she has joined up with Nomi of her own will. Believing there is something more to this, Haru tells Takumu about the incarnate system, suggesting they should find a way for him to learn it before facing Nomi again. As Haru grows fearful of the dark power inside him, he calls up Kuroyukihime for a little bit. As Haru and Takumu believe they may be able to learn something about the incarnate system from Yuniko, Scarlet Rain. Haru finds himself under suspicion over the camera found in the girl's shower room.
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, explaining the different skills that can be performed with them. As the type of skills an avatar can learn depends on the user's personal traumas, Takumu explains how he was bullied in elementary school, even leading to getting a scar, which gave Cyan Pile the weapons it has. As Yuniko begins training Takumu, Haru is joined by Yuniko's ally, Blood Leopard, who takes him to Akihabara to investigate how Seiji hides from the matching lists. They arrive at the Akihabara Battle Grounds, a fighting arena for Burst Linkers which is also having troubles with an unlisted Burst Linker called Rust Jigsaw.
Leopard decides to enter herself and Haru into a tournament to lure out Jigsaw, also explaining to Haru how overusing the incarnate system can bring him closer to darkness. Sure enough, Jigsaw comes to challenge them, but Haru and Leopard manage to overcome his tricks and defeat him. After the match is finished, the two return to the real world to seek out Jigsaw's user, but end up losing him. The next day, Haru decides to talk to Chiyu, who had started participating in battles with Seiji, swearing to take back what Seiji had stolen from her. As Haru analyses what information he had learnt so far, who deduces from Jigsaw's actions that Seiji was using an illegal brain implant chip to hide from the matching lists. As Haru confronts Seiji with this knowledge, Seiji suggests they settle things in an all atakes battle in which they wager all of their burst points.
On the day of the battle, Chiyu asks Haru and Takumu to join them on the field so she can see the battle to the end. As the sudden death duel begins between Haru, Takumu and Seiji, Haru is ambushed by an ally of Seiji's, Black Vice, who possesses a deceleration ability. As Haru remains trapped, Takumu takes on Seiji using his new incarnate ability, Cyan Blade, managing to overcome Seiji's Demonic Commandeer ability and slice off one of his arms. Seiji explains that he was bullied by his older brother, driving him to become more powerful and get his revenge. He then proceeds to take Chiyu hostage and torture her, causing Takumu to lose his will to fight. As Haru laments the hopelessness of the situation, he manages to regain his resolve and break free from Vice's grip. As Seiji prepares to finish off Takumu, he is stopped by the arrival of Kuroyukihime, who managed to enter the field from Okinawa using the item she got from Sulfur Pot. Engaging battle with Vice, Kuroyukihime encourages Haru to stand up and defeat Seiji.
Haru equips the Gale Thruster and engages in aerial battle with Seiji, managing to deal a strike before it runs out. Although Chiyu uses her Citron Call on Seiji again, healing him, Seiji's wings suddenly disappear and return to Haru. Using the combined power of his wings and the Gale Thruster, Haru deals the finishing blow to Seiji. After the battle, Chiyu reveals her ability isn't healing but is in fact the ability to reverse time, which she used to return Haru's wings to their rightful owner, revealing she only sided with Seiji in order to level up her ability to pull it off. As Seiji becomes desperate, Vice reveals to Seiji that his brain implant chip will disappear once Brain Burst is removed before taking his leave. With nothing left to save him, Seiji is finished off by Haru and loses his Brain Burst. Afterwards, Chiyu reveals it was her who told Kuroyukihime about their situation and decides to join their legion. After Kuroyukihime returns from Okinawa, she visits Haru, who explains everything and wishes for her to stay by his side. Back at school, Haru is cleared of suspicion whilst Seiji has lost all of his memories relating to Brain Burst. Afterwards, Haru takes Kuroyukihime to finally reunite with Raker, where it is revealed that Kuroyukihime's name, or at least nickname is "Sachan".