After the Shogun nearly falls victim to an assassination attempt by unknown forces, a plan is put into motion to help him escape Edo. Several diversions, each with body doubles set off in different directions, guarded by those loyal to Shigeshige. However the loyalty of some remains uncertain...

Zenzou and the Iga clan have betrayed the Shogun! Their forces are ambushed from all sides as forces loyal to the shogun desperately fight back.

After it becomes clear that the Iga clan didn't actually betray the Shogun, Gin and co are taken to their village and learn the truth about the Shogun's deep involvement with the clan in the past.

As Sarutobi attempts to rescue the critically wounded Zenzou, Odd Jobs, Hijikata and Kondou desparately fight back against the ruthless Yato clan, trying to get the Shogun to safety. Meanwhile, Takasugi seeks out Gintoki to end things once and for all.

Past histories are finally confronted for Gintoki and Kagura as they face off against Takasugi and Kamui.

As Gintoki and Takasugi continue their frenzied fight, the past they shared together with Katsura is revealed, as well as the fate of their teacher, Shouyou.

As various conflicts draw to their conclusions, the Tendoshu swoop in to finish off the survivors.

With the battle over, the survivors each go their separate ways. With Nobunobu appointed the new Shogun, Shigeshige and his retainers retreat to Kyo to regroup. For those left in Edo, there may be dark times ahead.