Bakumatsu

"We still have things we need to do." Takasugi Shinsaku and Katsura Kogoro have finished tending to Yoshida Shoin`s grave in Hagi. They return to Kyoto in order to correct the flow of time thrown off balance by the legendary treasure, the chronometer. Suddenly, the earth trembles and the sky splits open, and the chronometer, which was supposed to have been destroyed, appears from a rift in space-time. Now with a will of its own, the chronometer starts going on an uncontrollable rampage! Standing in their way is Takasugi`s fated rival, vice commander of the Shinsengumi, Hijikata Toshizo, who was lost in the previous battle!! Commander of the Shinsengumi, Kondo Isami, refers to the shocking existence of a new Mugensai.

"Several sightings of ghost lights have been reported around Kyoto." While Shinsaku and Katsura are searching for the vanished chronometer they get asked by Tokugawa Yoshinobu to look into rumors of a strange phenomenon. At the same time, having recently assumed control over the giant castle Susanoo, the new Mugensai, with a mysterious boy named Mori Ranmaru serving as his aide, orders the Shinsengumi to look into any connection between the chronometer and the ghost lights. Why have the Shinsengumi once again changed masters to the new Mugensai? In the midst of the constant chaos, the space-time rifts start appearing again! What is the truth behind these peculiar burning red lights?

"In a village outside Kyoto, villagers are being attacked and killed in succession by an unknown creature." Sakamoto Ryoma tells Shinsaku and Katsura. Katsura, who has been collecting information on mysterious incidents and paranormal phenomena that are being reported around Kyoto in his quest for the chronometer, tries to head out to the village to verify the rumors, but Takasugi suddenly seems reluctant to go. On Ryoma`s suggestion, Katsura takes Izo along with him to the village. The unusual pairing wind up dragged into puzzling incident and they find themselves facing one of the twelve commanders of Susanoo!

"I`ll just have to punch the crap out of Hijikata-san when he does show up." Captain of the 1st division of the Shinsengumi, Okita Soji, keeps mentally going over what happened during the Susanoo Incident when Hijikata went missing. While looking for the chronometer, Soji and the Shinsengumi once again encounter Takasugi and the others. A space-time rift opens up during this encounter and Soji is sucked into it. When Okita awakens, he finds himself in a Kyoto without the giant castle of Susanoo in the distance. He is standing before another Ikedaya when he hears a very familiar voice call out, "We`re here on official business!"

"We have returned from scouting." Tokugawa special agents Hyo and Kasumi make it back to Yoshinobu and the others full of energy after having finished their reconnaissance mission of the giant castle Susanoo. These two young girls work hard to complete their missions despite their youth. Mikado observes the girls one day and notices their interest in konpeito candy after they have an encounter with some local children. Mikado then decides to set off on his own to get some. Worried for Mikado`s wellbeing, Yamazaki sends Hyo and Kasumi to keep an eye on him. Meanwhile, a new commander of Susanoo follows Mikado like a sinister shadow.

"Katsura has been acting weird lately." Katsura has begun to investigate the whereabouts of the chronometer on his own since its presence hasn`t been felt for quite some time. Realizing something is going on with Katsura, Takasugi consults with Ryoma about the situation. Takasugi stubbornly insists that he will get the chronometer back from Katsura and carry out Master Shoin`s dying wish to return time back to normal. But Ryoma questions if that timeline truly is the "right" one and in the midst of their argument a strange phenomenon occurs and they rush outside. Once outside the duo notices that everyone and everything seems frozen in place!

"If the chronometer is used to return time to its original course..." Suspicious that Ryoma may already have gotten ahold of the chronometer, Katsura confronts him and reveals the reason he is trying so hard to get the chronometer before Takasugi does. Despite knowing Katsura`s motives, Ryoma gives him the slip, and with the chronometer indeed in his possession. Meanwhile, Takasugi learns from Seimei that he is the one who created the chronometer. In order to find out how the chronometer was created, Takasugi travels back to the past with Seimei`s unusual powers.

"What is he going to do with the chronometer?!" Katsura discovers that Ryoma indeed has the chronometer. In a clash with Izo, Katsura demands to know what Ryoma plans to do with the device, but in an instant, Ryoma uses the chronometer to turn back time. Izo calls into question Ryoma`s careless use of the chronometer and in the midst of their skirmish they are startled by a bright flash of light. The chronometer shows the duo a future that hasn`t happened yet. Takasugi, having sensed the chronometer, hounds Katsura with more questions about his suspect behavior, while Yoshinobu arranges a secret meeting with Kondo through Yamazaki. During the meeting, Yoshinobu reveals his secret plans for the future of Japan.

"They are both opponents I`m closely linked to, after all." Okita and the Shinsengumi discover Ryoma and Izo`s hiding place, and Mugensai joins them as they pursue the pair. Ryoma and Izo hatch a plan to trick Mugensai with a fake chronometer and split up, but before they can carry out that plan, they are found by Mugensai and the Shinsengumi. Meanwhile, Yoshinobu turns to a still bickering Takasugi and Katsura for help in rescuing the captured emperor. Suspecting that he knows the true identity of his master, Kondo speaks with Mugensai.

"Toshi...!" Kondo and Okita try to help free their beloved friend from the evil spell of the chronometer. However, Mori Ranmaru appears and arrests both Kondo and Okita, throwing them in a cell for treason. At the same time, Takasugi and the others sneak into the giant castle Susanoo in order to free the emperor, but come across a hidden surprise. Ryoma has also come to the castle seeking revenge for his fallen friend, Izo and to retrieve the chronometer. As things come to a head, Katsura finally admits to Takasugi the reason he has been secretly looking for the chronometer alone.

"Kyoto has vanished?" Right after finally getting rid of the twelve commanders of Susanoo, Takasugi and the others find themselves surrounded by a vast plain. Seimei explains the shocking truth that Susanoo Castle has traveled back to the distant past, and taken them with it! They`re not alone though, Mugensai has also been pulled back in time with the castle. Takasugi squares off against his masked foe, but a lucky blow reveals a familiar face hidden underneath. Meanwhile, back in the other time period, Sakamoto stares at the remains of the castle and clutches the chronometer as he contemplates what to do to bring back his friends.

"You`re not going anywhere!!" Having become one with the giant castle Susanoo, the hulking figure of the castle and Mugensai stalks towards Lake Ogura to make his plan to plunge Japan into a world of unending war a reality. However, Takasugi, Katsura, Yoshinobu, and the Shinsengumi stand in his way and put their lives on the line to prevent his plan from taking fruit. The longstanding conflict that Takasugi and his companions have been struggling to deal with finally seems to be near its end! How will their feelings surrounding the chronometer be resolved? And what new age will be awaiting them when this is all finished?