The year is 20XX, an era where the metaverse has become a seamless part of everyday life. The story follows Ikki Ichido, a remarkably gifted elementary school student at Shinkai Academy who possesses the unique ability to perfectly replicate any skill he witnesses. Despite his talent for achieving excellence in any field, Ikki has never found a passion that truly holds his interest, always moving from one challenge to the next in his quest to become the coolest person in the world. He dismisses the obsessions of others, such as his friend Hagumi Hanamaki, who tries to interest him in the real-world marvel of the Shinkansen bullet trains.

During a visit to Omiya Station, Ikki and Hagumi encounter a verbose upperclassman named Taisei Onari, a middle school student and self-described railfan who enthusiastically praises the design of the E5 Series Shinkansen. Their meeting is abruptly interrupted when a giant, mysterious monster known as an Unknown suddenly appears in the real world, grabbing Hagumi in its massive hand. Taisei reveals himself to be a driver of the Shinkalion E5 Hayabusa, a giant robot that transforms from a bullet train, developed by the secretive Evolution Railway Development Agency (ERDA) to combat these threats. After Taisei successfully rescues the two children, a second, more aggressive Unknown attacks, leaving Taisei critically injured.

With Taisei incapacitated and the ERDA systems hacked, preventing reinforcements, the unconscious senior driver is all that stands between the children and the rampaging Unknown. In a moment of desperation, Ikki takes the controls of the Shinkalion E5 Hayabusa. Though initially his Aptitude Value is too low to activate the machine, he recalls Taisei’s faint words that a truly cool person is someone kind who has something to protect. By using his mimetic talent to perfectly trace Taisei's movements and replicate his fighting spirit, Ikki successfully pilots the Shinkalion, synchronizing his aptitude exactly to the injured driver’s level and destroying the enemy. He thus becomes the new, unlikely pilot of the E5 Hayabusa, diving into a hidden war that spans both the real and virtual worlds.

As Ikki takes on this new responsibility, a mysterious boy named Atos is introduced, who appears to be controlling the Unknown from the shadows and becomes a key figure of intrigue. The narrative develops a notable arc focusing on the relationship between Ikki and the enigmatic Atos. In an effort to deepen this bond, which is crucial to the unfolding conflict, Ikki decides to take Atos on a trip to Kyoto, leading to new encounters and further complications in their fight against the Unknown. The story follows Ikki as he learns that true heroism is not about personal glory, but about the connections he forms and the people he chooses to protect in a world where the lines between reality and the metaverse are constantly blurred.