At the Bakufu's palace, the Shogun was about to drink the tea made by his sister when Ayame suddenly broke the cup with a kunai, revealing that the tea had been poisoned by someone. As a result of this failed assassination attempt, the Shinsengumi and the newly-back Oniwabanshuu were given a mission: To escort him out of Edo. However, Hattori refused to return to the Oniwabanshuu and cooperate with the others.
As planned, there would be three doubles of the Shogun: one stayed in Edo, one went by sea and one by land, whereas the real one would travel by air. The Yorozuya, Shinsengumi (except Okita) and Ayame protected the last double, who was actually Gintoki. While so, on the spacecraft carrying the Shogun, Hattori turned up and beheaded him before Maizou's eyes. Soon, many shinobi disguised as soldiers began attacking all four groups. On air, Okita slashed the traitors and protected Soyo-hime from Kamui and the other Yato people before Hattori gave them the Shogun's head and the spaceship crashed.
As of the land group, Ayame said that the shinobi attacking them were from Iga Clan, where the Oniwabanshuu originated. Three leaders of Iga were Fujibayashi Gaimon, Momochi Rappa and Hattori Zenzou. There, believing that the Shogun was dead, Fujibayashi said that he would kill everyone and reduce the Shogun's power afterwards. Nevertheless, the Shogun, still well and alive, appeared and ordered everyone to attack the insurgent. It was revealed that Momochi and Hattori had put a double in his place to fake his death and planned to kill Fujibayashi, who had surrendered Iga to the Harusame.
Not long after, the Harusame and Takasugi visited Iga, intending to destory the village and kill Hattori. Unbeknownst to them, he had planted the bombs on their ships earlier, resulting in explosions on every of them. While so, Abuto soon found out that the Shogun was still alive, and shinobi were sent to fight against the Harusame's Yato people and to make time for the Yorozuya and him to run away.
Meanwhile, on another fleet, Maizou and Soyo-hime were revealed to have survived after escaping in a pod, which was altered by Okita to trick the Harusame into thinking that they were dead. Though, Okita himself was put in a deep coma due to his injuries. There, Maizou informed Matsudaira that Hattori had beheaded a double, not the real Shogun. He knew that by checking the body for a scar, which the Shogun got while saving one of his doubles, Kagemaru, in his childhood. In return, Kagemaru became the beheaded double to save his life.
On the Harusame's fleet, Ayame rescued an injured Hattori, while other members of the Oniwabanshuu came to aid them. In Iga, after a while of fighting, the Yorozuya had to bring the Shogun out of there through a tunnel, whereas Momochi, Kondo and Hijikata stayed back and continued fighting. Ayame also brought Hattori to there, where she was stabbed and shot by Takasugi and Kamui, respectively, as the Harusame were waiting for the two inside the tunnel. The Yorozuya and the Shogun then arrived at the right time and fought fiercely against them.
During the fight between Gintoki and Takasugi, many flashbacks of their past had been shown:
Takasugi was frequently mistreated by his noble family and got bored with the current education.
Katsura was a poor, orphaned, yet excellent student who got a scholarship in the school Takasugi was in.
After meeting Yoshida Shouyou and visiting his school, Shouka Sonjuku, the two tried to protect it from the officials and were eventually admitted by him.
Gintoki was Shouyou's very first student before he opened his school.
Gintoki was also Shouyou's executioner, as a result of having to choose between killing his teacher and letting his comrades die.
Takasugi's left eye was destroyed by Oboro.
Meanwhile, as fight ensued between Kagura and Kamui, the two siblings battled against each other, with the younger eventually losing. Nevertheless, the fights were all disrupted by the Tendoshuu's arrival, and Takasugi was stabbed by Oboro, who got stabbed back in the left eye. The Tendoshuu then announced Nobu Nobu becoming the next Shogun and dethroned Shige Shige. In reaction, Shige Shige went hiding in Kyou to plan a resistance, where he was assassinated later.
Characters in order of appearance
- Tokugawa Shige Shige
- Tokugawa Soyo
- Tokugawa Sada Sada (flashback)
- Sarutobi Ayame
- Hattori Zenzou
- Sakata Gintoki
- Kondou Isao
- Hijikata Toushirou
- Matsudaira Katakuriko
- Shimura Shinpachi
- Hitotsubashi Nobu Nobu
- Takasugi Shinsuke
- Yamazaki Sagaru
- Rotten Maizou
- Okita Sougo
- Fujibayashi Gaimon
- Momochi Rappa
- Kijima Matako
- Kawakami Bansai
- Takechi Henpeita
- Umibouzu (flashback)
- Yoshida Shouyou (flashback)
- Saitou Shimaru
This story arc is largely based on the Second Chōshū expedition and the preparation of the Boshin War. In this period, the 14th Shogun, Tokugawa Iemochi (who Tokugawa Shige Shige was based on) died, the historical Kiheitai reformed and the Joui factions unified to overthrow the Bakufu not long before the Meiji's Restoration.