While Marie and Naoto managed to foil the plan of the Kyoto Grid purge, they did not find RyuZU's sister AnchoR. Marie was going about her day when an illegal shortwave radio transmission reaches her. Behind the inflammatory content aimed at Marie, there is yet another layer of intrigue...

As soon as Naoto hears that RyuZU's sister is slumbering in the basement, he agrees to help. After numerous trials, they finally make it to the lower floors of the Core Tower and continue their work, but the countdown for the purge keeps ticking. Under pressure, Naoto is forced to make a decision that could end up in him losing RyuZU!

Marie has a chance encounter with RyuZU, who she thought was broken all this time. When she finds out that it was Naoto who repaired her, Marie asks for his help to prevent the purge of the Kyoto Grid. On their way to the Core Tower, Marie finds out who is behind all the attacks on her.

The Meisterguild sent genius clocksmith Marie Bell Breguet to investigate the anomaly at the Kyoto Core Tower, while there, however, she notices that the army seems to be up to something. Meanwhile, RyuZU arrives at Naoto's school as a transfer student. The entire school is up in arms because the loser Naoto is with a girl as beautiful as RyuZU...

While Naoto and Marie are attempting to reconstruct the world, AnchoR goes off on her own to stop the Yatsukahagi's rampage. RyuZU, Halter, Vermouth are all fighting their own battles while hoping that the two could make a miracle happen. Can the two geniuses stop Gennai from destroying the world that Y had created?!

Along with Marie's old school friend, Houko Hoshinomiya, Naoto and the others observe the coup d'etat when they get a report that the Japanese government is going to use the Tall Wand against the Yatsukahagi. As the time draws close to the impact of the Tall Wand, Gennai, the mastermind behind the coup d'etat, fires the Yatsukahagi's main cannon. The two geniuses, Marie and Naoto, face a new challenge in order to stop Gennai's rampage.

In order to demagnetize the Akihabara Grid, Marie and Naoto decide to take over the Pillar of Heaven, which is the center of all the grids in Japan. With the help of a weapon housing Halter's mind, they overrun the Sakuradamon Grid and take Souko Hoshinomiya hostage. They then make a big announcement, but what's the aim behind that?

It's been 1000 years since Earth has died and been reborn as the Clockwork Planet. One day, in Kyoto, a black box nearly crushes Naoto Miura, a nerd who surrounds himself with clocks and gears. Inside that box is a beautiful automaton called RyuZU. Since she is not moving, Naoto sets out to repair her, relying only on "sound".

Second place school Todo-dai Sagami continues to impress... Not only are they strong, but their clever play produces advantageous situations for them throughout the game. Their barely legal plays and words mess with the Jinko players... The game begins going in Jinko's favor once Ebumi joins the game, but the stronger Sagami team tries to take the game back by force!! Do the savage Sekizan and the rest of the Jinko team have any chance at winning?!

As the members of the rugby team are feeling the results of their training camp, Komori arranges a practice match against Todo-dai Sagami. Their opponents placed second at the Kanagawa prefectural preliminaries... Sekizan is fired up at the prospect of facing just the type of opponent he hoped for! But Yoshida, the team's advisor, calls the rugby team's activities mere "ball games." Jinko versus Sagami... Will Yoshida see ball games or something more?!

For Gion, who joined the rugby team after being charmed by tackling, rugby = tackling. Even during an intrasquad match, Gion neglects teamwork and the basics in favor of tackling and tackling and tackling... Komori has some harsh words for Gion! Gion becomes depressed... Concerned, Iwashimizu tries to cheer him up... Will his voice reach Gion?!

With their new coach Komori, the new and improved Jinko Rugby Team begins the second day of their training camp. Contrary to Gion's excitement, a fight breaks out between teammates. The first thing the hot-tempered sore loser Ebumi ever became passionate about... was rugby. And because of his attitude, he can't tolerate the lukewarm approach of his teammates!

The Jinko rugby club's training camp has begun. As the team engages in intense practice, a lone man appears and tells them they're wasting their time. The harsh words of former national team coach Komori Shingo leave the team at a loss. Meanwhile, Sekizan asks him what the team is lacking. Will Komori become the savior of the leaderless Jinko rugby team?

It looks like Keijo may be making a comeback in their game against Keijo thanks to prodigal first-year Oharano Estugo. However, their opponent is one of Kanagawa's top four teams. The match begins going poorly under their opponents' skillfull assault. In order to change the flow of the game, Sekizan subs in the amateur Gion! Will Gion have a chance to shine in his very first match? Jinko VS Keijo finally comes to a close!!

The practice game against Keijo High, one of Kanagawa's top four teams, begins. Iwashizumi faces off against Miyuki Atsushi, the friend he injured during middle school. Will Gion's words reach Iwashizumi's soul as he's unable to wholeheartedly take on his old friend? As the fierce battle rages on, Sekizan's unparalleled determination to win leads him to tackle his rival Taira Tadakazu...!

The bad blood between Matsuo and the other third-years remains... but right now... right now making the "Strongest Team in Kanagawa" standing before us remember our name comes first!! Despite their inconsistent coordination, Jinko desperately holds on, finally drawing that man to the field... The Jinko VS Ryoin game heads towards is magnificent conclusion!

The team's game against Ryoin has finally started!! They may be the second string, but Ryoin is still the strongest team in Kanagawa! Jinko is tossed about by Ryoin's refined play... is what they were expecting, but the Jinko team that has gotten stronger over the past few months fights on equal footing against Ryoin! As the fierce battle continues, an ominous atmosphere surrounds the third-years...?

With the Ryoin game coming up tomorrow, Iwashimizu spends the night anxious. Miyuki realizes his friend's emotional state and shows up at his inn. When Gion, who had been training at the field alone, joins them, the three of them begin a secret training (?) session. While hanging out with friends and teammates, Iwashimizu realizes anew how fun rugby is, and all trace of anxiety towards tomorrow's game disappears from Iwashimizu's heart!!

With the Ryoin match coming up, the stagnating Gion practices tackling with Kasuga, Hyosu, and Ise! On the complete opposite end of the spectrum is Susa. Susa tells Oharano he doesn't know how it feels to just barely make the cut. Oharano becomes enraged by Susa's words, and the two end up in an argument...

During a moment after their match has ended, Gion and his teammates run into a group of Ryoin players at a crepe shope. Yoshida's request pays off, and Ryoin agrees to play against Jinko in two days. With the upcoming match against Ryoin, Gion heads out to the field at night to get in some "secret training." However, someone has beaten him to the field... Kifune is already practicing there!