At the Bakufu's palace, the Shogun was about to drink the tea made by his sister when Sarutobi Ayame suddenly broke the cup, revealing that the tea had been poisoned. As a result of this failed assassination attempt, a plan to bring the Shogun to Kyou was come up with the help of the Shinsengumi and the newly-back Oniwabanshuu. However, Hattori refused to take part in the plan.
As planned, there would be three doubles of the Shogun going on different ways, whereas the real one would travel by air. On land, the most dangerous route, the Yorozuya, Kondou, Hijikata and Ayame protected Sakata Gintoki, the double. While so, on the spacecraft carrying the Shogun, Hattori turned up and beheaded him before Maizou's eyes. Soon, many shinobi disguised as guards began attacking all four groups. On air, Okita slashed the traitors and protected Soyo-hime from Kamui before Hattori gave the Harusame the Shogun's head and the spaceship crashed.
As for the land group, Sacchan confirmed that the shinobi attacking them were from Iga Clan, where the Oniwabanshuu originated, and led by Iga's three leaders: Fujibayashi Gaimon, Momochi Rappa and Hattori Zenzou. There, believing that the Shogun was dead, Fujibayashi revealed to be an insurgent against the Shogun. Nevertheless, the Shogun, still well and alive, appeared and ordered everyone to attack him. It was revealed that Momochi and Hattori had faked his death and planned to kill Fujibayashi, who had surrendered Iga to the Harusame.
Not long after, the Harusame and Takasugi Shinsuke visited Iga, intending to destory the village and kill Hattori. While so, Abuto 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 to evacuate the Shogun out of Iga through a secret tunnel.
Meanwhile, on another fleet, Maizou and Soyo-hime had survived after escaping in a pod with Okita's help. Though, Okita himself was put in a deep coma due to his injuries. There, Maizou informed Matsudaira that Hattori had beheaded a double instead. He knew that by checking the body for a scar, which the Shogun got while saving one of his doubles, Kagemaru, who, in return, became the beheaded double.
On the Harusame's fleet, Ayame rescued an injured Hattori, and they were aided by the Oniwabanshuu. Bringing Hattori to the tunnel, she was stabbed and shot by Takasugi and Kamui, respectively, as the Harusame had been waiting for them. The Yorozuya and the Shogun then arrived at the right time and fought fiercely against them.
During the fight between Gintoki and Takasugi, their past had been brought up:
- In their childhood days, Takasugi was frequently mistreated by his noble family and got bored with the current education, while Katsura was a poor, orphaned, yet excellent student who got a scholarship in the school Takasugi was in. After meeting Yoshida Shouyou, as well as his very first student - Gintoki, and visiting his school, Shouka Sonjuku, the two tried to protect it from the officials and were eventually admitted by him.
- During the Joui War, the trio was captured and Gintoki, after being forced to choose between his mentor and his comrades, executed Shouyou, thus keeping his promise with Shouyou to protect his comrades, yet breaking another one with Takasugi to protect Shouyou. As a result, an enraged Takasugi ran to Gintoki and was stabbed in the left eye 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 Hitotsubashi 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
- As of November 2014, this arc has surpassed the Yoshiwara in Flames Arc, which had 18 chapters, to become the longest Gintama arc ever. However, in July 2015, it was surpassed by its following arc, Farewell, Shinsengumi Arc.
- This arc explains Tokugawa Shige Shige's origins before becoming the Shogun and marked his last appearance at death in Lesson 524.
- 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, and the historical Kiheitai reformed.