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 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.

While the others go to a festival in town, where they also run into Nae, Kaito helps Kona continue her search for cheaters, introducing her to Airi and telling her about the Kimijima reports. The next day, the club assembles the top and bottom halves of GunBuild-1 together, completing its construction, although Akiho worries that she hasn't heard from Misaki. As a large amount of people come for GunBuild-1's first test run, Kaito pilots the robots and gets it to take its first steps. However, due to the outdated construction which also results in the diesel engine failing, it fails to leave an impression on the crowd, much to Akiho's dismay.

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.