The Shogun is beheaded by Hattori, the Kihetai start their ambush and Sougo confronts Kamui for a showdown.
The episode starts with a flashback where a ninja history class being taught by Zenzou's father (it is about the birth of the Oniwabanshuu who were some Iga ninja that helped the first Tokugawa Shogun and were rewarded by being his personal warriors) was interrupted (again) by his lazy, apathetic son. Back in the present, the land group is resting in a dango shop with the Yorozuya Shogun eating and being obnoxious. Wakikaoru complains about the job to Sarutobu, wonders whether or not Shige Shige will be able to bounce back from this and tells about her wistfulness of Hattori not taking the job due to his personality. The bespectacled ninja refutes Wakikaoru assessment of the ex-Oniwabanshuu leader but is interrupted by two ninja calling out to her.
Another flashback shows a young Shige Shige telling a young Hattori and Sarutobi that he hoped that both he and the Oniwabanshuu can work together to help the country, cutting back to the present after Hattori decapitates the Shogun with a paralyzed Maizo watching in shock. Hattori pick up the head, apologizing for both of them doing their duties, then claims himself as a traitor before almost leaving. The airship is immediately attacked and surrounded by airships belonging to the Harusame Yato Division, led by Kamui and Abuto. At the same time, the water route is also attacked by ships led by Takasugi and the Kiheitai. A retainer desperately wonders how did the enemy know of their plans until he is killed by the navigator. At the same moment on the land route, the two ninja tell Sarutobi that some of their scouts were killed and they should change course since there were traitors within the group. Sarutobi, Hijikata, Kondou, and Gintoki immediately kill their attackers (which includes the two ninja), with Sarutobi revealing that since the attackers were also body doubles, their enemies were also using ninja.
Back with the attacked airship, Kamui watches the infiltrated ninja kill off most of the retainers, impressed with their abilities and wishing to get involved with the fighting. Abuto once again chastises his boss for his blood-thirsty nature and they both watch as the ninja chase an unprotected Soyo into a corridor believing this will be her death. Instead they are all killed by Okita who adds a few more kills when more ninja attack. He was asked by Hijikata to sneak aboard the airship in the (correct) belief that there may be trouble and the Shinsengumi captain relishes in the fighting... until Kamui abruptly lands on one of the ninja surrounding Okita and Soyo. On the water route, the Kiheitai storms on board the vessel and the Shogun double is the only one left when he is confronted by Takasugi. Before the double is killed by him, Takasugi reveals that he was able to amass a large ninja force and has attacked all three routes with them.
On the airship, Kamui kills off the rest of the ninja, so he and Okita can battle, since he believes he's found a kindred spirit in the teen. The two fight in a brutal battle and almost finish each other off until the ship explodes. Soyo tries to find Okita and Maizou arrives, asking the princess to flee. The girl demands to know where her brother is but Okita knocks here out, telling the retainer to flee while he tries to buy (very little) time for them when some Yato surround them. They are all interrupted by Hattori who tells the Yato and the Kiheitai to stand down as he had the head of Shige Shige. They do so as the airship starts to sink while Kamui acknowledges Okita's prowess.
On the land route, the remaining retainers, Hijikata, Kondou, Sarutobi, and the Yorozuya are all attacked by white-clad ninja and separated. As Sarutobi saves the Yorozuya, she reveals that their attackers all came from the Iga, who unlike the Oniwabanshuu, were mercenaries and hold no loyalty to the shogunate. The four run away as Sarutobi wonders who amassed such a force except for the three leaders of the Iga:
- Fujibayashi Gaimon (who had captured and buried Kagura)
- Momochi Rappa (who had captured Shinpachi and hanged him by his ankles)
- and Hattori who was working with the Kaiheitai-Yato division alliance.
The Iga surround Sarutobi and GIntoki and Rappa threatens to kill Shinpachi and Kagura, unless they bring the shogun. Gaimon reveals that the Iga village was attacked by the Yato Division six months ago and forced to cooperate with them with the distinction of becoming the new Oniwabanshuu in the new government. Rappa then gives word that Hattori had just killed the Shogun, hogging the glory. Gaimon doesn't care as he crushes Kagura underfoot and orders his men to kill everyone, before losing his balance. It turns out an Iga ninja cuts off Gaimon's leg that was on Kagura and another ninja cuts the chain holding up Shinpachi. The two ninja are really Hijikata and Kondou who adds that there is one person they follow orders from. Gaimon is horrified to see the ninja group and Rappa turning against him, the bandaged woman also adds that she was also following someone else's orders. This person, dressed as a ninja, arrives and to Sarutobi's the Yorozuya's and Gaimon's shock, it's Shige Shige!!