After being forced to flee to Edo, the members of the Shinsengumi are disillusioned. Aside from the Shogun's behavior, they also face personal problems. Kondou is still recovering from his gun wound, Okita is bedridden, Sanna slips into madness, and Hijikata fights to keep the Shinsengumi together. No matter how dangerous the battle, there is no stepping down. As the flames of war threaten to engulf them, they must prepare to return to the battlefield once more or risk losing more than just their lives in Hakuoki: Record of the Jade Blood.
After suffering defeat and retreating to Edo, the Shinsengumi must fight the urge to simply give up. Once Kondou returns, he tells everyone that they are going to fight the Imperial Armies in Koshu.
Kondou’s pride leads him to make more bad decisions, leading to the deaths of countless men in a battle they had no chance of winning. Just as the Shinsengumi are trying to retreat, Kodo appears with an army of furies!
Kaoru reveals his true identity to Chizuru and explains his diabolical plans. Once the battle is over, the rift between Nagakura and Kondou grows worse. Facing internal struggle and external conflict, what will become of the Shinsengumi now...?
A terrible secret about where a fury’s powers come from is brought to light. The Shinsengumi HQ gets surrounded by enemy soldiers and someone must serve as a decoy. But knowing the price one must pay for using fury powers, who will go?
Hijikata leads the siege on Utsunomiya Castle, where he gets into a gruesome fight with Kazama. Elsewhere, Harada runs into Shiranui, who informs him of Kodo’s next evil plot.
Harada and Shiranui fight Kodo and his ranks of furies to protect Edo from their bloodlust. Elsewhere, Okita dedicates every ounce of his strength to fighting a squad bent on killing Hijikata while he is still weak.
Saito leads the Shinsengumi to Aizu, where he is placed in charge of a small troop of willful soldiers. Can Saito earn their trust and respect while also waging a war?
The final showdown between Hijikata and Kodo’s furies has come to hand. Sannan, Hijikata and Heisuke fight the entire Fury Corps on their own. Some days later, the Shinsengumi decide to move to Ezo, but Hijikata orders Chizuru to stay behind.
Thanks to some help from Otori, Chizuru is once again reunited with Hijikata. But their happy time together is short-lived, for despite their best efforts, it is only a matter of time before the Imperial Army strikes at Hakodate.
The end of the long war is about to come to an end. Hijikata confesses his feelings for Chizuru. Now that he has her, he has a reason to live even after the war is over and the Shinsengumi are no more. But can he survive these last battles...?