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Taisei Onari, a railway-loving second-year junior high school student, transfers to Shinkai Academy in search of clues about his missing older sister, Ina. Just when he meets Ryota Kuzuryu and Mai Ome, and is excited about the railway club they are affiliated to, Unknown emerges in the city for the first time in ten years. Incidentally, Taisei is found possessing high Aptitude Value as a Shinkalion driver, and is forced to make the decision to fight.

Taisei rides Shinkalion E5 Hayabusa and goes into his first battle. Although he is forced to struggle with unfamiliar driving, he manages to Vehicle Combine under Takanawa's instructions and somehow succeeds in defeating the Unknown. However, Taisei feels responsible for not being able to protect the pedestrian bridge where he and Ina watched the E5 series road transportation when they were young.

Taisei, who has officially become a member of the Railway Club, is given a tour around ERDA by Takanawa, and learns the reason why Shinkalion was developed, as well as the fact that his missing sister, Ina, was once involved in the development of Shinkalion. Meanwhile, the Unknown shows up in Ryota's hometown, Tsuruga this time. Ryota wants to protect his hometown with his own hands, but he doesn't have enough Aptitude Value.

In preparation for more Unknowns to appear, Taisei stays in Tsuruga and enjoys the railway museum he once visited with his sister. Meanwhile, Ryota is training alone to raise his Aptitude Value. Ryota has a strong admiration for the Shinkalions because a Shinkalion saved his life when he was young. Although he feels regretful that he was unable to protect Tsuruga with his own hands, he still hides his true feelings.

In preparation for further Unknown attacks, ERDA continues to search for driver candidates for the Shinkalion E6 Komachi. Meanwhile, Taisei and Ryota form a group with Akane for a class presentation, but quickly fall apart. Although Akane appears cool and confident at school, he has a certain problem.

Akane was injured due to being involved in an accident when the Unknown appeared, but after examination, it was found that he possesses high aptitude as a Shinkalion driver. ERDA members hope to welcome him as the yet-to-be-discovered driver of the Shinkalion E6 Komachi, but Akane declines the invitation. Taisei and Ryota desperately call out to him to fight together, but...

An Unknown that appeared between Nagoya and Mikawa-Anjō was defeated by the Shinkalion N700S Nozomi. Its driver is Ten Uotora, who is one year younger than Taisei and the others, and is a member of ERDA's Tokai Headquarters. Taisei and his friends travel to Nagoya for a joint training with the Tokai Headquarters. They will be training together in a simulation with Ten, who is known as a "genius driver" who has by far the highest Aptitude Value, but Ten doesn't seem to be serious.

Ten disappeared when his Aptitude Value dropped significantly. Because of this, Ryota and Akane get into an argument. What flashes through Ten's mind is an incident that occurred with his friends a year ago. Apparently that has something to do with the reason why Ten stopped being serious…. Seeing Taisei and his friends fighting together and trusting each other even though they were arguing with each other, Ten takes a certain action.

Although ERDA's server is accessed by Ina's account, tracking fails. Taisei consults Takanawa, saying that he is concerned that the places Unknown has appeared so far are all places of his memories with Ina. Meanwhile, Shion Goryokaku, the driver of "Shinkalion H5 Hayabusa", is found, and everyone is happy to have a new driver joining them, but Shion seems to be hiding something.

Taisei and the others head to Hakodate to meet Shion, who says, "There's something I want to discuss in person." Mai and Vina are eager to support the romance between Shion and Yuki, but when they arrive at Shin-Hakodate-Hokuto Station, a shocking truth awaits them. Shion, who is unable to meet Yuki due to certain circumstances, asks Akane to pass on a message to her so as not to hurt the only friend she has made since attending school in the Metaverse.

The "three-person four-legged relay" is a traditional competition at Shinkai Academy's sports festival. Taisei, Akane, and Ryota will be participating as representatives of their class. Cheered on by their friends, the three practice hard, but Taisei is distracted by the mysterious voice he heard in Hakodate and can't seem to concentrate. Meanwhile, the Black Shinkansen appears between Ueno and Ōmiya. ERDA finally succeeds in capturing the Black Shinkansen, but...

The voice coming from the Black Shinkansen, "Phantom Shinkalion", belongs to the missing Ina. Taisei is so shocked that his Aptitude Value drops and he is no longer able to ride the Shinkalion. While Akane, Ryota, Ten, and Shion set off to various places to defeat the Unknowns that have appeared across the country, Taisei, whose Aptitude Value has not yet recovered, traps himself inside the Metaverse. Then, someone appears before him.

Ina declares war on ERDA, demanding unconditional surrender. ERDA considers Ina to be an enemy for leading the Unknown, and their hostility becomes unwavering. Taisei sees how much Ina has changed, but he still can't give up his desire to believe in her. In order to stop Ina, he decides to ride on Shinkalion and fight again.

After Ina regains consciousness, ERDA interrogates her. Takanawa speculates that whoever retrieved the "Phantom Shinkalion" was the one who brainwashed Ina. Meanwhile, at Shinkai Academy, Taisei and the others are shocked to hear that the Railway Club may be disbanded. Just then, Takanawa receives the notification that a candidate for the driver of the "Shinkalion E8 Tsubasa" has been found.

After finding out that Ganma is the driver candidate for “Shinkalion E8 Tsubasa”, Takanawa tries to recruit him, but is flatly refused. Meanwhile, the Railway Club's survival is in jeopardy. Taisei and his friends try to persuade Ganma, who is the student council president, to keep it alive, but Ganma says, “If you want to protect it, you should have the power to match that.” These words seem to have something to do with his past.

Ganma, who has become a driver, joins the Railway Club. Hearing that the Railway Club members will be eating lunch together, Ganma comes to the club room, but Akane is not there. Meanwhile, at ERDA, Ina develops the "SRG System" to combine the three units, "E5 Hayabusa", "E6 Komachi", and "E7 Kagayaki". The condition for success is that the "SRG Values" of the three people match. So the three immediately start a simulation, but...

While Akane, whose SRG Value ​​does not match, is filled with guilt, Taisei and Ryota are also worried about Akane, who has been going to the Track-and-field Club more often. Furthermore, when they hear Akane say that he is leaning more towards track and field, the relationship between the three becomes strained. Meanwhile, a mysterious enemy suddenly appears - "Hades Shinkalion". Taisei and his friends are forced to struggle against its overwhelming strength, and try out the Three Car Combination as their last hope...

Akane still can't match Taisei and Ryota's SRG Value. While he ponders the reason, Kakeru asks him to officially join the Track-and-field Club. Taisei and Ryota, who have been watching secretly, decide to send Akane off, but the Hades Shinkalion appears again. Ganma, Ten, and Shion, who happen to be present at ERDA, immediately fight back, but...

Taisei meets a person who calls himself "Delta" in the Metaverse and is introduced to Ido, Delta's friend and promotional AI for the SCMaglev and Railway Park. Delta is someone Taisei admires, as he is building his ideal railway in his own Metaverse. That same night, the members of the Railway Club visit the summer festival. The drivers enjoy the food stalls, but Taisei struggles to make a good cut. Meanwhile, the Unknown attacks again….

When Taisei and his friends arrive at Kokura Station in Kyushu, they are greeted by Tsukumo Umikaze, the driver of Shinkalion N700S Kamome. Taisei and his friends immediately begin simulation training. However, during the training, Tsukumo's Vehicle Combination fails. The cause is not Tsukumo, but the new operators Katsuki and Adachi. Ochiai from the Ōmiya Command Office is appointed to be in charge of training these two.

Tsukumo, Taisei and others board a high-speed boat in order to send Kai and Suzu to their hometown, Iojima. While confronting the Unknown that suddenly appears, Shinkalion N700S Kamome successfully Vehicle Combines with the ERDA Ferry, but is forced to struggle in the battle at sea. When Taisei and his friends ask Tsukumo why, it seems that he is traumatized by the sea.