Horikawa Kunihiro has manifested as a Sword Warrior and is joined by Izuminokami Kanesada, a warrior who served under the same master as him. With a single goal in mind, the two rush through the mountains...

With the newly arrived reinforcements, Saniwa and his unit push through the castle to find out why the Time Retrograde Army is here in this era. However, time runs out, and their Master Saniwa must return to the Citadel. He leaves Kanesada in charge of the unit, but will he be able to unite everyone and solve this mystery?

As the mystery is unfolding, the Second Unit is now having trouble keeping themselves together. A small fight breaks out between Kanesada and Mutsunokami. Kunihiro suggests to Kanesada that they work separately in two teams. Will it be wise to split the party?

A new mission brings the Second Unit to Edo, where the tension between the pro-shogunate forces and the Imperial army are so hot, you could almost set it on fire. With plenty of room for the Time Retrograde Army to alter history, will Izuminokami and his team be able to stop them?

A mysterious figure appears before Yagen. Is he friend or foe? Yagen might be surprised. As Horikawa and Tonbokiri continue to fend off that giant ootachi, the others board the warship to join Yagen. Will they figure out the Time Retrograde Army's plan in time to stop them from succeeding?

As Kanesada watches Edo, everyone is teleported back to the Citadel. While the Second Unit recuperates for the time being, they are still waiting for that person to wake up. At this time, Kanesada seeks help from the eccentric and mysterious First Unit Captain.

The First Unit mobilizes! With the old captain watching over this duplicate of a new captain, what kind of powerful monster could be waiting for them? As Honebami joins the First Unit as their newest member, he encounters a being from his past...

Honebami thinks the First Unit has successfully completed their mission, but their captain tells them that they have one more mission. Meanwhile, at the citadel, Izuminokami was still in turmoil from his previous mission, but Horikawa cheers him up. He then goes around to everyone in his unit, and asks them a certain question...

No more casual clothes and relaxing at the Citadel! The Second Unit mobilizes with a fresh start, and lands in Kyoto, 1866. Here, they need to protect one of the Touken Danshi's former masters. However, due to a certain rule, they need to avoid seeing their former master if possible. Will they be able to protect him while not getting into contact with him?

Even though their mission is complete, Saniwa asks the Second Unit to stay in that era. While continuing to monitor Sakamoto Ryoma's safety, Horikawa begins to question why the Touken Danshi can't see their former master, and how would he himself react if he ever sees his former master again...

Horikawa Kunihiro has gone missing. The Second Unit realizes they haven't seen him since the plum tree incident. Izuminokami and Mutsunokami try to search for him, but Izuminokami finds Kunihiro in the strangest of places...

Kunihiro has decided to pursue his own loyalty. What could that even be? In the midst of chaos, Saniwa descends upon Izuminokami and Mutsunokami. After briefly discussing the situation, he takes them to the area where the Battle of Hakodate is taking place. What could Saniwa want to do here?

The conclusion of the Battle of Hakodate and the fate of Hijikata Toshizou unfold. Was Kunihiro able to pursue his loyalty? Was Izuminokami able to protect history? The season comes to a conclusion as the Time Retrograde Army unleashes its force of 1,000 upon Hakodate!