An amnesiac woman named Tari wakes up in a lab and finds herself in Silica City. She discovers she has a cybernetic arm and learns that she is a Meta Runner, people who replace their limbs with cybernetic enhancements to improve t heir video game performance. Tari walks into a TASCorp store and finds a speedrunning arena in a back room. There, she sees a Meta Runner, Belle Fontiere, attempting to set the world record for the game Ultra Jump Mania by executing a glitch. Belle performs the glitch correctly but misses the goal pole, thus losing the record. Once everyone leaves, Tari picks up Belle's controller and starts playing. Belle belittles Tari at first, but soon begins to question who she is and where she learned to play the game. Tari's rapid finger movements cause her to suddenly lose consciousness. When she wakes up, she finds herself on an island. She is then attacked by Theo, the protagonist of Ultra Jump Mania, and Tari learns she has been transported into the game. Meanwhile, Belle calls in her boss, Lucks, to investigate. He begins to berate Belle for her failure in the speedrun, but he soon becomes intrigued by Tari. After seeing that she is in the game, Lucks urgently calls in his TASCorp scientists.

Inside Ultra Jump Mania, Tari manages to convince Theo that she isn't an enemy. Theo tells Tari that she is on Simpleflip Island and then proceeds to leave her behind. Tari catches up to him and follows him on a platforming adventure. On the way, Tari discovers her Meta Runner vision, which gives her data and shows her how to pass obstacles. The duo eventually comes across a horde of palm tree monsters known as Facepalms. Theo gives Tari a pineapple hammer and the two engage the enemies. Back in the real world, Lucks and his scientists continue to investigate Tari. Belle is unimpressed, but Lucks says that Tari's ability could be the future of gaming and that he could give her ability to everyone, pointing out that he invented the influential Meta Runner arm. In the game, Tari and Theo defeat the enemies. Lucks arrives in the game, speaking through a version of Theo. Lucks asks Tari about her abilities, and the TASCorp scientists begin drilling into her arm, causing her agonizing pain. With a burst of energy, Tari returns to the real world and is shocked to discover that Theo came back into reality with her.

Tari and Theo are confronted by Lucks, who attempts to convince Tari to work for him at TASCorp. Tari refuses and, with help from Theo, manages to escape the speedrunning arena. Belle tries to chase after her, but Lucks stops her, saying they can't be seen chasing a civilian in public. They take what they have and Lucks promises to deal with Tari. Meanwhile, Tari and Theo hide in an alleyway in Silica City, with Tari saying they are in real danger and Theo's video game abilities don't work in the real world. They hide inside a streaming pod, where Tari has a flashback of a mysterious scientist and Theo inadvertently gives up their location to Belle by starting a live stream. Tari is confronted by Belle and is eventually captured, while Theo fights off the TASCorp scientists and escapes. Theo then sees Tari getting loaded into the back of a TASCorp van and begins to cry. However, a mysterious Meta Runner approaches Theo and tells him not to worry.

Inside the back of the TASCorp van, Belle tries to calm Tari down, telling her they only plan to extract her abilities to give them to other TASCorp Meta Runners and saying that she herself has been through worse. As Tari begins to wonder what will happen to Theo, the van is hit by a car. Tari escapes the van and sees Theo in the car. She gets in and it drives off, with Lucks and Belle in pursuit in the van. Inside the car, Theo introduces Tari to Lamar Williams, a Meta Runner who is driving the car with a game controller. He gives Tari a hoodie that causes signal interference, believing Lucks put a tracking device in her arm. After a car chase through the city, the trio eventually comes up against a closed barrier set up by Lucks. Tari uses her Meta Runner vision to analyse the situation and takes the controller from Lamar; she escapes by using a fallen billboard to propel the car over the barrier. Lamar promises to take Tari and Theo to a safe place. Meanwhile, Lucks tells Belle that he no longer just wants Tari's powers, but wants her, which Belle calls creepy. Elsewhere, Lamar brings Tari and Theo to a secret hideout in a ramen shop. There, Tari and Theo meet Lamar's friends: Sofia Porter and the Meta Runner Masa Shimamoto.

A flashback shows a spy camera watching Belle at the speedrunning area before Tari shows up. In the present, Lamar explains that he and his crew were using the camera to gather some intel on Lucks and TASCorp on the day of the speedrunning incident, but changed their plans when they saw what happened with Tari. Sofia tells Tari and Theo that their group, MD-5, are trying to take down TASCorp for all the horrible things they have done. Tari is hesitant to join the group, claiming she wants nothing to do with TASCorp at all, but Theo convinces her to help MD-5 since they gave them shelter. However, Masa refuses to let Tari and Theo join unless the former can prove herself via a first-person shooter game called Battle Blaze, to see how well she can handle a human opponent. Tari is easily beaten by Masa several times before Sofia inspects Tari's Meta Runner arm and causes her to warp into the game. Meanwhile, at TASCorp, Lucks has Belle search a research facility for info after noticing a strange emblem on Tari's outfit, and he investigates the corrupted copy of Ultra Jump Mania that Theo came out of in the meantime. Belle then wanders into a messy and abandoned lab. Back at MD-5, Tari begins to improve; seeing her potential, Masa gives Tari some advice on how to beat him by clearing her mind. After narrowly losing to him, she is assisted by Theo, who entered the game as well, discovering that he can use his game abilities as long as he is in a game. Sofia brings them out, and Masa tells Tari that, while she has a lot to learn, they have a place on the team for her. Theo then begins to glitch out due to being out of his game for too long, and Masa urges them to return him to an Ultra Jump Mania cartridge. Back at TASCorp, Belle comes up empty and begins to give up, until she finds a memory card containing video logs about "Project Blue".

Tari gets Theo into MD-5's Ultra Jump Mania cartridge, but the presence of another Theo causes the game to glitch and boot the two out. Sofia deduces that Theo needs to return to his own cartridge, prompting Masa to suggest "Operation Silent Demon" to get the cartridge from TASCorp. Inside the destroyed facility at TASCorp, Belle watches a video log from the crazed Dr. Sheridan on Project Blue, an AI system he is working on capable of beating any video game once it is implemented into a human host. The final log shows an accident with the test run, causing an explosion that presumably kills Sheridan and his unseen assistant. After hearing the assistant's voice, Belle is distraught. At MD-5, Sofia and Masa explain their scheme to hack into TASCorp's servers to obtain and release their private records and files to the public, damaging Lucks's image. To do this, they would enter an underground competition hosted on TASCorp's servers; Tari would enter the game and crash it by executing a glitch, which would give Sofia time to hack into the servers and download the data, as well as place an order for Theo's cartridge. Lamar is skeptical about the plan, but concedes after Tari agrees to it. Back at TASCorp, Belle shows Lucks sees the footage from Dr. Sheridan, explaining that the Meta Runner that Sheridan experimented on was her best friend Lucinia, who they had thought went missing. Examining the footage's details, Lucks notices Sheridan execute a cheat code on a controller. Lucks inputs the same code, causing the corrupted Ultra Jump Mania game to show the emblem for Project Blue.

In Tempest (the magic-focused battle royale game for TASCorp's underground competition), Tari, Theo, Lamar, and Masa begin training for the competition. They teach Tari how to collect spells to use attacks and teach her what the glitch is, which is going through the floor by falling into it at 55 km/h at a 36 degree angle, thus crashing the game. Tari learns that to pull the glitch off, she needs to jump off the top of a mountain in the game and use a wind spell to propel herself downward to gain enough momentum. Tari continuously tries to pull it off, to no avail. In a flashback, Belle is struggling to pull off a newly discovered glitch in Ultra Jump Mania when she is visited by her friend Lucinia, who gives her encouragement. Back in the present, Belle questions the connection between Project Blue, Tari, and Lucinia's apparent death. When Lucks's search provides no answers, he suggests that Belle obtain answers from Tari herself. Back at MD-5, Tari grows discouraged over her repeated failures. Theo and Masa give Tari some words of encouragement, and Tari is finally successful in pulling off the glitch. Masa tells them that, now that they know how to pull the glitch off, they need to be trained in physical combat, because in the competition, they'll have people attacking them.

About a week later, the day has come for the Tempest tournament. Tari, Lamar, and Masa sneak Theo and themselves into the competition. Tari starts to have second thoughts, but Masa and Lamar tell her that this is their best chance at pulling this off. As the game starts, Tari warps into the game, but is pulled into a void where she sees Lucinia. After she recovers, she wakes up on the raging battlefield. MD-5 starts gathering spells, using Lamar's forcefield and Masa's kunai. The group is then confronted by an elite team, which forces them to take a defensive stance. Lamar uses a teleport spell to get them to safety on a cliff. Lamar questions whether Tari is alright given she unexpectedly passed out at the start of the game, but she insists she is fine and Masa suggests they focus on performing the glitch. Their discussion is interrupted when they are attacked by the elite team from before, who knock Tari off of the cliff. Tari falls into a collapsed building and is attacked by the enemy team. Before they can finish her off, the rest of MD-5 arrives to assist her, and they go on the offensive.

MD-5 prepares to take on the enemy team, with Masa taking the lead and the others flanking the support members. They take out three of the enemies, but Theo is taken out after sacrificing himself to protect Tari, and the leader escapes. In the real world, it is revealed that the leader is Belle, who recognises Masa. Lucks, on a call with Belle, reminds her that the goal is to take out Tari. MD-5 gets to the top of the mountain. Tari prepares herself for the glitch, but the group is attacked by Belle, who takes out Lamar. MD-5 then realizes that TASCorp is onto them. Masa attempts to convince Belle to back down, but she refuses and reveals to Tari that Masa was once a team captain for TASCorp, but was decommissioned a year ago for hacking into Lucks's private server to prove his theory that Lucks killed Lucinia. Masa and Tari engage Belle and almost gain the upper hand, but Belle restrains Tari under a building and makes Masa overload his Meta Runner arm trying to defend Tari. Belle takes out Masa and Lucks tells her to finish off Tari, but she disables communications with him so she can privately interrogate Tari.

Tari tells Belle she doesn't know how her abilities work, but Belle reveals she no longer cares about Tari's abilities and angrily interrogates her about Lucinia, thinking she killed her despite Tari's objections. Belle begins torturing Tari and Lamar considers giving up, but after encouragement from Theo, Tari agrees to tell Belle everything she knows to get her to stop, only to evade her and execute the glitch despite Belle's efforts to stop her. Back in the real world, Masa and Theo commend Tari, while Lamar urges everyone to evacuate the arena. The group tries to escape, but they are cornered by a furious Lucks and the TASCorp security personnel, who subdue Tari, Lamar, and Theo. Lucks yells for Sofia to show herself, shooting off Masa's cybernetic arm and threatening to shoot him in the head, but a tearful Sofia arrives just in time despite Masa encouraging her not to. Lucks takes her tablet containing the server data and has his scientists clear it and destroy any backups. When Sofia says she just wanted to know what happened with her sister, Lucinia, Belle reveals the footage of the explosion, against Lucks's orders. Sofia breaks down and asks why Lucinia was with Sheridan, and Belle says to ask Tari, pointing out that the Project Blue logo is also Tari's logo. Masa's trust in Tari diminishes, but she insists she knows nothing. Lucks prepares to imprison MD-5 for life, but Tari offers to join TASCorp on the condition that Lucks lets everyone else go. Lucks reveals that he discovered MD-5's plan by using Theo as a spy camera via the corrupted Ultra Jump Mania cartridge. After Lucks traps Theo in a frozen state in a memory card, he threatens to destroy him if MD-5 causes trouble again or Tari starts to show signs of disloyalty. Lucks lets MD-5 go and leaves with Tari, who promises that she'll be fine.

In a post-credits scene, Belle discovers Sofia's phone in a bin, which has a backup of the data from Sofia's tablet, and she makes eye contact with Sofia, who is being escorted out. As Belle leaves, Lucks asks for a subject update on an earpiece. Health statistics are listed and a woman whose condition is stated to be stable is shown in a cryogenic freezer.

Six months after the events of Season 1, Belle and Tari are playing a match in a video game. After their win, the two are driven back to TASCorp by Lucks, who talks to an interviewer about Tari's imminent addition to TASCorp's main Meta Runner lineup in two weeks. After the interview, Lucks warns Tari to perform better at her debut match. Back at TASCorp, Tari is escorted back to her room while she views the harsh treatment of TASCorp employees. Back in her room, Tari demands Lucks to allow her to see Theo to make sure he is still safe. Lucks shows her Theo on a screen, who is trapped in a featureless room. While talking to Theo, Tari promises him that they'll see MD-5 again, and Lucks hastily ends the call. Meanwhile, in the "low tier" of Silica City, Lamar and Sofia walk through an alleyway to find Masa, who had abandoned MD-5 after the events of Season 1. Masa brushes them aside at first, but Sofia reveals that she saved a backup of the TASCorp server data onto her phone. However, her phone is at TASCorp with Belle, who unsuccessfully attempts to hack into it. Fellow TASCorp Meta Runner Evelyn Claythorne bursts into Belle's room to complain that Tari is getting exhibition matches instead of her. Evelyn then angers Belle by insinuating that Lucinia abandoned TASCorp. Belle promises to Lucinia and Tari promises to Theo that they'll figure something out.

Lucks talks to Theo, who is annoyed at him for trapping him. Lucks tells Theo they are working on a way to allow him to leave safely and gives him a chair, but Theo uses the chair to clip out of the room and lands in the TASCorp server. Lucks tries to stop him by deploying a data partition and quarantine programme, both of which Theo avoids, though the latter causes him to fall into an unknown file. Meanwhile, Tari and Evelyn are practicing a game called Hidden Heroes, with Belle overseeing them. Evelyn gets the edge over Tari and finishes her off. When Belle looks at the results of their match, the screen glitches and Theo lands on the screen, asking where he is, to Belle's shock. However, the quarantine programme catches Theo and drags him away. Back in Theo's prison, Theo asks Lucks if the deal to get him out is still available, but Lucks turns the screen off. Lucks reprimands his scientists and orders them to monitor Theo closely. Meanwhile, Evelyn openly complains that she has to share her debut match with Tari. The two bump into a TASCorp scientist, who is playing an anime dating simulator game called Pocket Gakusei. Evelyn mocks him and confiscates the game, but Tari gets an idea to contact Lamar (who is an otaku) via the game. In Masa's rundown house, Masa, Sofia, and Lamar discuss how to access the server backup on Sofia's phone, which Sofia thinks Belle is trying to get into. Glad that Belle finally came to her senses, Masa asks if they can just send her the encryption key, but Sofia explains that TASCorp has a stronger firewall, and if they send anything to Belle, Lucks will get tipped off about the phone. Lamar brings up that Tari and Theo are also trapped at TASCorp, but Masa angrily dismisses them as Theo was a spy camera and Tari was involved with Project Blue. Lamar and Sofia are able to convince Masa to help save Tari and Theo when they remind him of their promise to keep the two safe, but Masa says he needs a new Meta Runner arm since his previous one was shot off by Lucks. Sofia tells Masa they are too poor to buy one but can win one instead.

Masa, Lamar, and Sofia return to the low tier of Silica City to win a new Meta Runner arm. They enter a tournament hosted by Marco, an old friend of Sofia's who resents Masa for his former career at TASCorp. Marco challenges Lamar and Masa to a game of Turbo Crash 9; if Marco wins, Lamar must give up his Meta Runner arm, but if Lamar and Masa win, they get a new arm for Masa. At TASCorp, Tari searches Evelyn's room for Pocket Gakusei and finds it, but Evelyn catches Tari before she can leave. Belle arrives and discreetly allows Tari to use the game as long as she doesn't tell anyone. Back with MD-5, Lamar controls the team's vehicle while Masa handles weapons. Marco eventually gets the upper hand, but Masa and Lamar defeat him in the end when his arms begin to malfunction and they win the match, much to Marco's anger as he accuses Masa of cheating. They get the arm and drive back to Masa's place; in the car, Masa acts dismissive when Lamar asks if he cheated, but he is holding the control bug device that he used to make Marco's arms malfunction.

Tari enters Pocket Gakusei in search of Lamar, but the search ends up being harder than she thought. Meanwhile, Belle visits Sheridan's abandoned lab and contacts Theo, asking him if he can obtain information about Project Blue from TASCorp's servers in exchange for helping him reunite with Tari. Theo agrees, and Belle takes control of him using a game controller to clip back into the server. In Pocket Gakusei, Tari's search comes up empty until she remembers that Lamar likes a character called Satsuki-chan, who she finds in the game. The character remains silent, and Tari learns she needs to fill up a relationship meter with her in order to talk to her. Back at TASCorp, Lucks catches Theo running around in the server again. Theo finds a Project Blue file thanks to a strange purple glow and begins downloading it for Belle, but he is attacked by Lucks's quarantine programme. Belle controls Theo to fight off the quarantine programme and defend the file. Belle inadvertently gives up her location in celebration of obtaining the file, forcing her to leave Theo behind before anyone finds her. Theo is caught again and Lucks puts him back in the corrupted Ultra Jump Mania cartridge, leaving him alone with enemies that he can't fight off due to the game's glitching.

In Pocket Gakusei, after sufficiently dating Satsuki-chan, Tari is able to get Lamar's profile from her. Tari sends Lamar a friend request, making contact with MD-5. Tari apologizes to Masa, saying she herself has a lot of questions like he must have, but Masa tells her they can sort that out after she's safe. Masa reveals they will help Tari escape during her upcoming show match. At TASCorp, Belle accesses the Project Blue file and sees footage of Lucks searching the abandoned lab shortly after the explosion, realising that Lucks knew what happened to Lucinia all along and was hiding it from everyone. Belle angrily leaves, swearing to avenge Lucinia. Tari is visited by Belle, who offers to help her and MD-5 expose Lucks. Sofia gives Belle the benefit of the doubt, but Lamar and Masa are not so keen on the idea, the latter saying Belle has let him down twice before and he cannot handle a third time. Tari convinces Masa to give Belle a chance; Masa agrees, but tells Belle that if she is on his team, she is to follow his orders. Belle reluctantly agrees to this as Masa begins to explain their plan for TASCorp's show match.

Lucks introduces Tari and Evelyn at the beginning of the show match, and Evelyn gives a long self-centered speech about how she never got the attention she deserved as the youngest child in her apparently famous family. Sofia causes a power outage and Lamar covertly replaces TASCorp’s Hidden Heroes cartridge with MD-5's cartridge, which will download the server data from the phone as long as the game lasts for at least twenty minutes. Meanwhile, Belle returns to the lab to play the corrupted Ultra Jump Mania, where Theo is still trying to escape the monsters. Theo is initially annoyed at Belle for abandoning him, but she tells him if she can beat the game, it will reset, ending the glitching and allowing Theo to get out of the cartridge and escape TASCorp via a link on Sofia’s phone. Theo reluctantly allows Belle to control him to beat the game. Back at the show match, Lucks explains Hidden Heroes usually pits two heroes against ten minions, but for the show match, Tari and Evelyn will face fifty minions. Lamar and Masa enter as two of the minions, intending to stall the game for as long as possible. Evelyn continuously complains about Tari’s tactics while Lamar and Masa take out several of their teammates. Tari asks why Evelyn hates her so much, and Evelyn explains that she trained for years only for Tari to show up and “ruin” it for her. Tari angrily expresses her wish for Evelyn and TASCorp to leave her alone, and Evelyn immediately abandons Tari, who has to face several enemies on her own.

Tari is able to take out all the enemies with Masa's assistance. They notice Evelyn watching them, and Evelyn calls Lucks to tell him that Tari is conspiring with the enemy team. Meanwhile, Belle tries to complete the glitched Ultra Jump Mania game but is stuck on a level due to the server download amplifying the corruption. Theo then sees the purple glow from before going through the level and copies its movement to make it to the flag area by clipping through a wall. Back with Evelyn, she says Tari cheating explains the power outage, Tari's weird tactics, and the friendly fire on the enemy team. Lucks then realizes MD-5 is at the match. Lucks attempts to activate security measures to stop MD-5, but is stopped by Sofia, who passes herself off as tech support at first. This does not faze Lucks, but Sofia threatens to make TASCorp go bankrupt by exposing their secrets, aided by the rumors already swirling about them. Lucks makes hand signals to Evelyn in her pod to defeat Tari in the game. Evelyn hits Tari from behind with her sword and engages her in one-on-one combat. Masa and Lamar deal with the rest of the players since Tari is sticking to the plan of keeping Evelyn busy. Tari tries to convince Evelyn to back down, but Evelyn instead targets everyone else on the enemy team to end the game sooner, eliminating Masa in the process. Tari rescues Lamar, who asks Masa what he's going to do next; Masa says he is getting ready for when this is all over.

Evelyn covers the arena with fog, wipes out the other enemies, stuns Lamar, and tries to take out Tari. However, Tari manages to defeat Evelyn with help from the same purple glow that helped Theo. Just as Evelyn is defeated, Sofia's download of the server data finishes. Sofia gets on the intercom and starts an emergency evacuation, while Masa tells Lamar to get Tari to safety while he causes a distraction. Masa tackles Lucks, while an enraged Evelyn physically fights Tari, who pushes Evelyn into her pod, locking her in with Sofia's help. Tari gets the cartridge and leaves with Lamar, despite her concern about Theo not being there, while Masa is subdued by TASCorp scientists. Masa wakes up in a TASCorp holding van with Lucks and Belle, who was found by TASCorp. Belle calls out Lucks for lying to her about Lucinia for a year and a half, but Lucks says that everything he did was to protect the company. Belle apologises to Masa for not believing him when he first turned on Lucks, and they have a flashback to the night before Lucinia's disappearance, in which Lucinia expresses doubt in her abilities since the attention at the time was on Masa (the leader) and Belle (the new hotshot). Meanwhile, Lamar takes Tari to Sofia for a reunion, and Tari and Lamar explain they cannot release the server data since Theo and Masa did not make it out. Tari then comes up with a plan in which they either win big or lose everything, to which Lamar and Sofia agree.

Sofia calls Lucks to threaten that she will release the server data; Lucks tracks her location and intercepts her. Lucks scans the Hidden Heroes cartridge and finds no abnormalities, realising it was the cartridge Lamar stole from the show match being used as a decoy, but discovers that Tari has used the other cartridge to warp into the server and get Theo out herself. Lucks takes Sofia into the van with Masa and Belle and begins driving back to TASCorp to reboot the server and stop Tari. Meanwhile, Tari and Theo traverse Ultra Jump Mania's final level, trying to use the glitches to their advantage and reach the end before Lucks reboots the server. Lucks calls Evelyn (still trapped in her pod) to offer a rematch. Tari and Theo see the final flag to complete the game, but are stopped by Evelyn, who takes the form of a massive monster known as the Glitchemoth and puts the flag out of their reach. She activates an infinite lives cheat and takes out Tari and Theo repeatedly until they each only have one life left. Tari comes up with a plan and uses the glitches to obtain a pineapple hammer like the one she used previously (see 1x02 “Out of Bounds”), resuming her battle with Evelyn.

By exploiting the game's glitches and working together, Tari and Theo eventually manage to incapacitate Evelyn and reach the flag, thus beating the game. Theo escapes the cartridge, but Tari is visited by the purple glow, which reveals itself to be Lucinia, and she tells Tari about her past. Back in the real world, with both Tari and Theo in Lamar's car, Lamar rams into the side of TASCorp's van, but is less successful than the last time he did so as they have upgraded their vans. Lucks holds Masa at gunpoint and demands that Tari give him the cartridge, but the data has already been released to the public with the news spreading quickly through the city, and an arrest warrant has been issued for Lucks. Masa fights Lucks and takes his gun, saying everyone will now know that Lucks is responsible for Lucinia's death. However, Lucks reveals that Lucinia is still alive, the explosion having only injured her. He explains that she entered a coma and was unable to recover due to parts of her consciousness being missing, having been lost to the server or merged into the AI that Sheridan was developing. He reveals that Tari herself is that AI in an artificial body, which she confirms, having learned this from the remnants of Lucinia that were in the server. Thus, the only way to revive Lucinia would be for Tari to sacrifice herself. However, the group still blames Lucks for everything he has done and tell Tari they value who she is now. After Masa considers shooting Lucks, the others convince him not to, but his Meta Runner arm suddenly starts malfunctioning and shoots Lucks anyway, killing him. Belle stays with Masa and urges the others to run, but they are offered a ride by Marco.

In a post-credits scene, Evelyn is returning home in a car when she receives a call from a man offering her Tari's abilities and an opportunity for revenge. When Evelyn questions the man, he responds that it is easy to hack into Meta Runner arms if one knows what they are doing, having hacked Masa's arm earlier, and reveals himself to be Sheridan, having survived the explosion in the lab.

A week after the events of Season 2, Tari, Lamar, Sofia, and Theo are being held captive by Marco and his crew. Still bitter about Masa cheating him out of a Meta Runner arm, Marco challenges the group to a fair and honest match of Turbo Crash 9, and if they win, they can go free. Meanwhile, Dr. Sheridan kidnaps Masa and Belle while they're en route to jail and warps their minds into his personal server, where he has an AI version of Lucks as a minion. Sheridan reveals to Masa that he hijacked his Meta Runner arm to kill Lucks, to Masa's fury. Sheridan asks them to be a part of his new Meta Runner team, but they refuse, angering Sheridan. In Marco's hideout, Tari tries to warp into the match, but Evelyn, under Sheridan's orders, intercepts her warp and forces her into a digital lab where Lucinia lies unconscious. Sheridan reveals that, now that Lucks is dead, Tari has served her purpose, and he begins performing surgery on Tari to get the data fragments of Lucinia's consciousness out and revive Lucinia, while Masa and Belle are forced to watch.

Theo is warped into Sheridan's server and makes his way to Tari, being spotted by Masa and Belle. Masa and Belle try and communicate with Theo, but he is unable to hear them due to Sheridan placing them in a soundproof room. Sheridan catches them talking, so Masa and Belle distract him by telling him they want to join his Meta Runner team. Theo manages to escape with Tari, but Sheridan has Evelyn chase Tari down and gives her a knife that will collect data fragments from Tari to complete the surgery. In Marco's hideout, Marco stops his match with MD-5 due to Tari and Theo's absence. Hesitantly, Marco allows Sofia to try and find them. Tari and Theo fight Evelyn in a room full of motionless 3D models of Meta Runners, including Lamar. Sofia is able to open a gateway for Tari and Theo to escape through. Though Tari throws Theo to safety, some of her data is extracted by Evelyn, and she falls out of the gateway and gets warped into an MMO game called Skybreakers, where a pirate character called Petey introduces her to Shipwreck Swamp, the starting area. Due to Evelyn stabbing her and extracting data, Tari passes out. Moments later, Evelyn arrives in Skybreakers too in a mechanical suit.

Tari wakes up to find that Petey has bandaged her up. He forces her to complete his tutorial for the game, but her skill is impaired due to her lost data. Evelyn confronts Tari at the end of the tutorial, but Tari defeats her with help from Petey, followed by help from Lamar, Theo, and Marco (though Marco is only helping because the others told him he could get revenge on Masa), with Sofia assisting from outside the game. Meanwhile, Sheridan trains Masa and Belle by having them play Battle Blaze against an emotionless Lucinia, who is awake thanks to Tari's data transfer but brainwashed. Belle's emotions over missing Lucinia, as well as Masa's anger over what Sheridan is doing to her, get the better of the two. Sheridan prepares for his master plan, which involves a control bug.

Tari continues to struggle in Skybreakers and is annoyed by Marco's patronising attitude towards her. The group arrives at the hub city of Vagabonds Landing, where players are unable to attack each other, in order to get better gear. Evelyn re-enters the game with Lucinia, using hacks that allows them to attack the other players while in the city. Lucinia battles Tari, but she briefly stops upon recognizing Sofia's voice, allowing Tari to take her knife and use it to get back the data fragments. Tari and her friends end up escaping on a stolen ship. Marco, seeing Tari's true skill, names her the captain of their ship, which Tari calls "the Bluejay". Meanwhile, Sheridan has used the bug to take control of Belle and Masa's minds, and he ominously asks which of them wants to go through their employee induction first as members of SherCorp.

Tari and her friends discover a way to reach Sheridan's server through a virtual backdoor and they explore the dungeon Scrapbeard's Fortress in search of it. Meanwhile, Sheridan uses control bugs to brainwash Masa and Belle to serve him after showing the former mental images reminding him of his guilt and trauma. Tari's group encounters a boss and must perform a death warp exploit in which they die at the exact same moment the boss does to go out of bounds. Meanwhile, Lamar goes back to fight Evelyn and keep her busy. During their battle, Evelyn taunts Lamar over not being able to make it in the big leagues, but Lamar admits he never wanted to, knowing what TASCorp did to runners when they no longer saw them as useful. Tari, Theo, and Marco pull off the exploit successfully, but Evelyn defeats Lamar and warps him into Sheridan's server. He ends up in the room where his model was being kept along with many other Meta Runners that Evelyn and Lucinia had defeated in Skybreakers. Sheridan appears with Masa and Belle, who are completely under his control.

Sheridan introduces his dangerous remote warping technology to warp Meta Runners into his server against their will. He intends to test it by forcing the Meta Runners already there to attack each other with an assortment of video game items. Tari and Theo search for the gateway to the server in a largely empty beta level in Skybreakers, and Theo tries to hide that his still unsolved glitching problem is getting worse. The brainwashed Masa and Belle enter Skybreakers to join Evelyn and Lucinia, but Lamar covertly follows them. Sheridan activates his global warp technology, warping every Meta Runner in the world into his server (except Marco, who is unaffected due to having built his arms from scratch without any corporate tech). Sheridan also reveals that he was the true inventor of the Meta Runner arm and Lucks took the credit for his creation. After Theo sails through a storm to reach the gateway to the server, Tari realises he is glitching again, much to her concern, and Theo admits he didn't tell anyone because he wanted to have fun with his friends and not have them worry about him. Evelyn's team catches up to them, but Lamar reveals himself and the two teams destroy each other's respawn points, ready for a final battle.

Tari and her friends face off against Evelyn and the brainwashed Lucinia, Masa, and Belle. Marco is sidetracked trying to get revenge on Masa, and after getting eliminated, he sets out to destroy Sheridan’s server to ensure the safety of the warped Meta Runners. Meanwhile, Theo confronts Evelyn by himself to buy time for his friends. Evelyn makes Theo disintegrate by essentially squeezing him to death and gloats to a distraught Tari about it, but this brings Masa’s mind back. He strangles Sheridan in the lab, who breaks free and stabs him in the neck with a screwdriver before Masa’s arm explodes, causing the device hooked to Belle to stop working. Belle helps Tari defeat Evelyn once and for all, and Sofia urges Tari to revive Lucinia before Marco destroys the server. Tari jumps through the gateway with Lucinia in pursuit.

In a post-credits scene, Lamar gets enjoyment out of throwing rocks at Evelyn’s armor after respawning back in Shipwreck Swamp.

Sheridan recovers and is about to stab Masa with a knife when he realises Tari has made it into his server. Tari is forced to fight Lucinia as she attempts to bring her back to Sheridan's virtual lab. Sheridan and Sofia fight for control over the server, assisting Lucinia and Tari respectively by providing various video game items for them to use. Though Sheridan seemingly gets the upper hand, Tari manages to reach the lab with the help of Sofia. Sheridan tries to freeze Tari in place, but Sofia reveals she has tracked Sheridan's location and given it to Marco, who is arriving now, forcing Sheridan's attention away. Tari decides to use the machine in the lab to sacrifice herself and restore Lucinia's consciousness, bidding a final goodbye to Sofia. Marco bursts into Sheridan's hideout and hooks Sheridan's own control bugs to his body, electrocuting Sheridan to death and destroying his server, thus freeing the Meta Runners. Sheridan's Lucks AI hints to Tari that she might be able to restore Theo before being deleted with the server, and after telling Lucinia to say thanks and goodbye to her friends, Tari performs the surgery just in time before the server is fully destroyed. Belle, Masa, and Lucinia all wake up and are happily reunited, with Lucinia and Belle sharing a kiss. Marco forgives Masa for his debt, as Masa has already lost his Meta Runner arm again, and the group leaves.

Evelyn is arrested for her crimes and the murder charge against Masa is dropped. Marco’s workers repair Masa’s Meta Runner arm, and Marco holds onto it for safekeeping, looking forward to a true rematch with Masa in the future. Sofia, Lamar, Masa, Belle, and Lucinia all return to the MD-5 hideout, where they mourn the losses of Tari and Theo. Masa places a picture of Tari and Theo, as well as Tari's hoodie and Theo's newly acquired cartridge courtesy of Belle, in the hideout, praising Tari for keeping MD-5 together. Sofia then eagerly takes Belle and Lucinia to their “initiation” into MD-5, to Belle’s annoyance and the others' amusement.

Tari and Theo are preserved in fragments of the old server, and Tari has taken everything she could from the server so that she and Theo can live happily and in peace together within, as they are too unstable to exist in the real world anymore. The series ends with Tari thanking her old friends for the adventure before she and Theo run off to play video games together.