Kaito Yashio and his friend Akiho Senomiya are the remaining members of their school's Robotics Club. After Akiho hands in a budget request to the staff room, both she and Kaito, who spends his time playing games on his PokeCon device, visit an old hangar containing a large robot the Robotics Club has been working on since its foundation, Gunvarrel, based on a popular robot anime whose final episode was never aired. The next day, the vice-principal agrees to give the Robotics Club their proposed budget on the condition that they win a robot tournament taking place in two week's time, with the club to be disbanded should they lose. As Kaito and Akiho contemplate if they can pull off such a feat, a mysterious girl is seen making a report.

Needing a robot for the tournament, Kaito and Akiho find an old Tanegashi Machine hobby robot in storage, only to find its batteries have run out. Akiho goes to see an old man named Tetsuharu 'Doc' Fujita to try and get some new parts, but finds they are too expensive. Kaito asks shopkeeper Mizuka Irei to look into any weaknesses Doc may have so he can lower his prices. This leads Akiho to meet Doc's granddaughter, Junna Daitoku. Although Junna fails to be much help, Akiho manages to get the parts needed thanks to an advanced allowance and a promise that they'll pay with the prize money. After repairing the robot, Akiho and Kaito work on controlling it, with Kaito also having to deal with Akiho's 'elephant mouse syndrome', an ailment she got following an accident seven years ago in which time fasts forward for her. Noticing her fatigue, Kaito agrees to be the robot's operator on the condition that she makes the controls similar to his favourite game, Kill Ballad.

Kaito and Akiho go with their teacher, Mitsuhiko Nagafukada, to where the Robo-One tournament is being held, though they have no hotel to check into. As Kaito practises with the robot, he experiences a strange sensation for a brief moment. The tournament soon begins and Kaito manages to use his tactics to get through the preliminaries and into the finals. Before the final match, Akiho starts to grow concerned about Kaito, who hadn't gotten a lot of sleep prior to the tournament. The final match soon begins against the reigning champion, Mr. Pleiades, whose robot has some fierce tricks up its sleeve. While Kaito's robot is at a disadvantage against Subaru's, Kaito suddenly experiences an inverse of the ailment Akiho has, slowing down time for him, and makes a counterattack, knocking both of them out, though this technically results in Kaito's loss. Upon returning home, Kaito has a brief encounter with Kill Ballad's creator, Frau Koujirou.

Akiho tries to get her father, who is the president of the Tanegashima Space Center, to fund their giant robot project, but her mother soon quenches that line of thought. Later, Kaito is called to meet with Frau Koujiro, whose real name is Kona Furugoori, to help her move into her dorm as she is transferring into his school. Following more intel from Mizuka, Akiho goes to see Mitsuhiko's uncle, who runs a candy factory, to request sponsorship for their robot. Meanwhile, Subaru manages to get Kaito's assistance for an upcoming Robo-1 tournament in Las Vegas. As Subaru questions about what Kaito did during the tournament, Kaito recalls an incident on September 11, 2010, in which he and Akiho were part of a mass fainting aboard a ferry, where they both contracted elephant mouse syndrome. Later that night, Kaito hears a strange voice coming from his PokeCon.

Becoming curious about the girl she saw the other day, Kaito hears from Junna about various sightings of the girl. As Akiho and Subaru deal with an interview for the Robo-One tournament, Kaito and Junna go to the beach, where they encounter the cadaver of a beached whale. Hearing that Junna has retired from the karate club, Kaito suggests she pay a visit to the Robotics Club. Later that night, Kaito hears the strange voice again, leading him to an abandoned room in school, where he finally encounters the girl through his PokeCon. This AI, named Airi, reveals herself to be an Iru-O app that had attempted to contact Kaito over the past 8 years. She then shows Kaito a hidden file, containing a log by one Kou Kimijima, predicting gigantic solar flares would occur on certain years. As Kaito ponders how many of those predictions turned out to be accurate, Mizuka has a strange reaction where she hears Kaito mention Kimijima's name.

As Kanna pops by the Robotics Club and agrees to join, Kaito recalls what Mizuka told him about how Akiho's sister, Misaki, was allegedly friends with Airi. As Kaito once again visits Airi later that night to hear more details, including how Kimijima created her, he follows a strange noise to an underground room, where he finds an EGI device used to send noises to outer space. As Kaito tries to find more from Airi's 'Sister Centipede' mode, he learns that Kimijima was murdered by someone. After enough hassling from Subaru, Kona decides to join the Robotics Club, agreeing to help him with his controls if Kaito helps to find a cheater running amok in Kill Ballad. Kona manages to complete the program in a few days whilst Kanna helps Akiho secure a sponsorship for their robot. As they practise the controls, Subaru is approached by his father, who doesn't take kindly to him taking up robots again.

As Akiho tries to think of a way to help Subaru, Kaito realises from Kanna that the noises he heard from the EGI Device was "Kagome Kagome", the lyrics of which had been e-mailed to millions during moments where PhoneDroids simultaneously froze. Afterwards, he goes to help Kona search for the Kill Ballad cheaters, receiving a device to detect cheating for if he encounters them online, before briefly running into Subaru, who wants to dispose of his robot himself. As Akiho delivers a broken part to Subaru, Kona reveals to Kaito that the Gunvarrel anime's last episode never aired because the staff died right beforehand, with the anime's director, her mother Minami Kogoori, suspected of murder. Subaru deconstructs his robot but agrees to keep helping the Robotics Club. Thanks to their sponsorship and some knowhow from Doc, the club receives the parts for the GunBuild1.

Kaito and the others are taken to JAXA, where Nae explains that JAXA wants to support the production of their giant robot. However, Akiho rejects their offer when they suggest they build a new one from scratch instead of completing GunPro-1. Later, Kaito works with Airi to find the location of a second report by Kikijima. As Kaito works to fulfil the conditions to gain access to the report, he ends up having to protect an antennae in the middle of a typhoon. As Kaito almost falls off the antennae tower, his EM syndrome kicks in, allowing him to pull himself up to safety, managing to protect the antennae. Kaito soon falls unconscious but he is rescued by Akiho, who was alerted to his position by Airi. After Kaito recovers and explains Airi to Akiho, Kaito manages to access Kikijima's second report, warning him about how Kagome Kagome is linked to a project to reduce the world's population to one billion.

As Kona becomes intrigued by rumors of Gunvarrel's last episode being leaked, she and Kaito go to solve the conditions for unlocked Kimijima's 3rd report, finding the tasks pretty tedious. As Kaito manages to beat the Kill-Ballad cheater whilst passing the time, Kona gets infected with a virus whilst trying to analyse the data. Later that night, Kaito tries to get information about Kimijima out of Mizuka, whilst Misa is sent by her higher-ups to investigate Kimijima's reports. The next day, after the gang use Kanna to record motions for the GunPro-2, Kaito and Kona manage to unlock the third report, which talks about plans to use a magnetic storm to destroy mankind, mentioning Misa's Exoskeleton company as being part of it. Upon arriving back home, Kona learns that the top three ranked Kill Ballad players had in fact died in their homes half a year ago.

Despite Misa's warnings, Kaito starts gathering flags for unlocking the fourth report. Later, Junna learns that Doc has been taken into intensive care, though he refuses to see her when she comes to visit. As Kaito hears from Mitsuhiko that Doc plans to close his robot clinic, he hears from Mizuka how the shop used to feature robots designed by him to appeal to kids until 11 years ago, when one fell on Junna, causing her to develop a fear of robots. Akiho, who refuses to let Junna resign from the club until she likes at least one thing about robots, decides to try and cheer up Doc by fixing up his old robots, one of which is required for Kaito to complete one of the flags. However, Junna is scared off when the robot that fell on her that day is reactivated. As Junna resolves to quit the Robotics club, Kaito shows her a photo he found in the shop.

As the group celebrate Nae's birthday whilst figuring out how to make GunPro-2 move, Kona has remained confined in her apartment for several months. As Akiho and Subaru task Doc with making a motor from the monopole they found, Kaito tries to make sense of the fourth report, which details a purported robot rebellion. As Kaito goes to Kona for help with programming the motor, she reveals there were subliminal images in the leaked Gunvarrel episode hiding a password for a site made by Kona's mother, revealing a message mentioning solar flares and something called Project Atom. Afterwards, Kaito unlocks the fifth report, predicting the extinction of mankind. Despite narrowly avoiding an explosion, Doc succeeds in cutting the monopole in half. Just then, a solar flare hits the Kanto region, causing robots to run amock and attack people. Meanwhile, Kona discovers someone has hacked her TwiPo account, framing her for the robot attacks.

As the robots continue to run rampant in Tokyo, Kona explains to Kaito that the login to their control panel has been altered by the hackers to require they defeat a Kill-Ballad CPU opponent. Struggling to beat the opponent, Kaito decides to try and force his slow-mo by pushing his body to its limits, but to no avail. Kona soon founds out the person behind the hack was one of the members from her development circle, Maguyan, who claims he was forced to do it as his family was taken hostage. Kaito soon realises that Maguyan has in fact been brainwashed. As Kona hears the support of her friends from the Robotics Club, she explains how she created Kill-Ballad to keep Gunvarrel, and her mother's memories, alive. As the police show at Kona's doorstep, Akiho, Junna and Subaru help lure them away, buying Kaito and Kona some time to beat the Kill-Ballad opponent.

As solar flares start affecting computers, people besides Kaito and his group become able to see Airi, who has begun acting weird lately. A planned maintenance on the Iro-O system that could potentially erase Airi means that Kaito needs to fulfill the conditions for the sixth report before Christmas Eve. After Kaito unlocks the sixth report, Airi states that she wants to go to Kimijima's house for her birthday on Christmas Eve. There, Kaito discovers a machine in his basement containing Airi's original human body. Airi explains how she was cursed with an incurable affliction and always spent her days bedridden, hoping for a White Christmas. She soon met Kimijima, who let her see the world through the Iro-O system. As Airi's condition worsened, Kimijima put Airi into a deep sleep in order to wait for a cure and created the program Airi to keep her company.

The gang complete the construction of the GunPro-2, using the monopole motors and a laser-activated fuelling system, and successfully put it through its first activation test. Shortly afterwards, though, Nae informs the group that they will be unable to use JAXA for a week as there are plans to launch a rocket. Whilst Kaito goes off to search for Kikijima's next report, the others run more tests on the GunPro-2, where Junna notices something odd about its walk cycle. As Subaru runs alongside it to figure out what is wrong, a sudden gust of wind sends the robot toppling towards him. Meanwhile, as Kaito finds the location of the seventh report, Mizuka confronts him, warning him not to pursue the reports. Just then, Kagome Kagome once again plays on their Pokecoms and a strange noise plays upon Mizuka answering it, causing her robotic legs to go out of control and work her towards a cliff edge.

After Kaito, Akiho and Mitsuhiko pay their respects to Mizuka, the vice-president announces that, following Subaru's accident, the Robotics Club will be disbanded and their cooperation with JAXA halted, ordering all the robots they've made to be dismantled. As Kaito, against his better judgement, goes to download the seventh report, he is confronted by Toshiyuki Sawada of Exoskeleton Inc., who questions him about Kimijima, though Kaito refuses to answer him. Afterwards, Kaito receives a call from Misaki, warning him not to show the reports to anyone. After having a nightmare about Misaki, Akiho tells Kaito that she intends to finish the robot and take it to the expo herself. Despite finding the notion ridiculous, Kaito agrees to hear her out if she beats him in Kill Ballad which, to her surprise, she manages to do. As such, Kaito agrees to help, with Doc and Mitsuhiko also providing their support.

Kaito and Akiho travel to the Tokyo Expo with their robot, where they discover they have to share a hotel room. As Kaito has nightmares that night, Akiho asks him to be a bit more open with his troubles. Whilst preparing for the expo, Akiho becomes excited when she hears Misaki will be at the expo promoting the Exoskeleton robots. Kaito decides to meet up with her in person in order to confront her about Mizuka's death, also talking about Kimijima, her meeting with the real Airi, who woke up in hospital the other day, and above all, her attitude towards Akiho. The Tokyo Expo soon begins with Akiho having a tough time impressing the crowd with the recent bias against Gunvarrel. Despite Kaito's warnings, Akiho goes to see Misaki, who is seen in a fully robotic suit. Just then Sawada appears and brings out a gun, shooting it when Misaki starts to run away.

As Sawada's first shot has no effect on Misaki and he starts unloading before being tackled by Kaito who urges Akiho to chase after Misaki. As the Kagome, Kagome tune soon starts playing from the Arena's PA, Akiho watches in disbelief as Misaki boards the Sumeragi and begins reeking havoc within the expo, by destroying the other robots. As the Sumeragi sets its sights on GunBuild-2, Akiho tries in vain to defend it and has another EMS seizure upon its destruction, followed by Kaito upon seeing Akiho's state before Misaki escapes. In the aftermath, whilst getting Akiho to safety, Kaito discovers a massive obelisk has appeared out of nowhere, which Akiho deduces to be the space elevator from the leaked Gunvarrel episode. As the Haneda and Narita Airports are shut down due to a massive solar flare which is blamed for the Expo's attack, Airi has a mysterious visitor in her hospital room as the Airi AI begins singing Kagome, Kagome from her Poke-Com.

As Mitsuhiko begins streaming the encounter via Iru-O, Kimijima reveals that on the day of the S.S. Anenome incident he had been planning on using the passengers as test subjects for a radiation experiment but was murdered by Misaki to save Kaito and Akiho when she caught onto his plans. Afterwards, Kimijima began appearing to her through the Iru-O network, threatening to reveal what she did along with Kaito and Akiho, forcing her to cooperate with his plan. Kimijima further states that he had threatened Airi in a similar manner and if it wasn't for Misaki's meddling, Project Atum would have occurred in 2015. Akiho questions Kimijima on whether Misaki still loves robots and he suggests that she still might, since she didn't stop playing Kill-Ballad. Akiho further vows that they will stop Kimijima and his plans using their giant robot and save Misaki whilst Sumio helps disarm Airi, who faints while Kimijima disappears.

Whilst everyone else works on fixing up the GunBuild-1, Kaito, Nae and Airi head to Kimijima's lab to retrieve data for the device Sawada gave him, although Kaito undergoes a seizure when he attempts to activate it. Just then, they are confronted by some armed droids run by Kimijima and Sister Centipede. However, Sister Centipede manages to have the droids shoot each other, only to be erased by Kimijima shortly afterwards. Meanwhile, as Akiho and the others complete the GunBuild-1, which she renames the Super GunBuild-1, she reunites with Ken'ichirō before learning of Kaito's condition. Despite his injuries, Kaito insists that he be Super GunBuild-1's operator, believing that the device Sawada gave him can trigger his Slow-Mo at will, giving him a chance against the Sumeragi. Akiho objects, however, believing using the device could kill him. Kaito assures her that he will help her meet Misa face-to-face again, giving her the Slow-Mo trigger.

Kaito arrives before Misaki, with the others helping to divert the missiles she fires using AR decoys, although Kaito is forced to use the Slow-Mo and sacrifice one of his pile bunkers to dodge the last one. Kaito manages to get up close to Misaki's Sumeragi and use the Slow-Mo to attack her with the other pile bunker. However, this knocks Misaki out and allows Kimijima to take full control of her as he divides the Sumeragi into a more mobile unit. After locking down the launch sequence, despite Nao and the other adults reclaming the control room, Kimijima launches an attack at the others forcing them to seperate, which leaves the Super Gunbuild-1 with only five minutes of power. Just then, Kona receives a program from Sawada that will erase Kimijima if they can get his avatar in the PokeCom's view, although it requires a reboot which leaves Kaito vulnerable.