With the help of Mutsunokami Yoshiyuki, Yagen Toushirou, Tonbokiri, Izuminokami and Saniwa head to the castle in pursuit of the Time Retrograde Army. Leading the charge, Mutsunokami witnesses the slaughter of the castle samurai at the hands of the Retrograde Army. In order to find out the Time Retrograde Army's true purpose behind the castle attack, Izuminokami and company must stay in this era to continue their investigation. Saniwa names Izuminokami Kanesada, Mutsunokami Yoshiyuki, Horikawa Kunihiro, Yagen Toushirou, and Tonbokiri as the Second Unit, and charges Izuminokami with leadership of the unit.

With the unexpected explosion of the steamship, the port is thrown into chaos. Despite Mutsunokami's best efforts to save the survivors on the ship, he vents out his anger and regret of not able to save everyone. As Mutsunokami is getting more emotional, Izuminokami is trying to convince him to listen to reason. The differences between the two Sword Warriors starts tearing the unit apart. Izuminokami splits up the unit to investigate the Roushi (Masterless Samurai) thinking the Time Retrograde Army will manipulate the Roushi and their anti-foreigner ideology for the Army's schemes. However, as Mutsunokami listens to the Roushi's wishes, he starts to worry about their safety.

The Second Unit protected the “Teradaya Incident” and kept history intact. Saniwa suspects more Time Retrograde Army members are in hiding, so the Second Unit stays in Fushimi to protect Ryoma Sakamoto from further dangers. Meanwhile, Horikawa is agonizing over his purpose as a Sword Warrior as his feelings for his former master, Toshizou Hijikata, grow.

The Second Unit has returned to the Citadel. Izuminokami and Tonbokiri sustained heavy injuries from their battle with the Time Retrograde Army, but they managed to protect the meeting. Though, Tonbokiri’s life-threatening injuries from fighting the Ootachi are so serious that even with Saniwa’s treatment, he remains in a comatose state. Meanwhile, Izuminokami questions his own ability to lead the unit after seeing his comrades, many innocent people, and the town he’s supposed to protect all suffer from the Time Retrograde Army during this mission.

The destination of the new Second Unit is Fushimi, Kyoto, year 1866. The Time Retrograde Army is attempting to attack Ryoma Sakamoto, the key person who formed the Satcho Alliance, thus interfering with the Teradaya Incident. The Second Unit must try to stop the Time Retrograde Army by following Mutsunokami’s plans. However, even though Mutsunokami purposely avoids contact with his former master, he ends up having to save Ryoma in his time of peril. Facing his former master troubles Mutsunokami with an internal struggle…

It is March, 1868. The Second Unit led by Izuminokami has arrived in Edo. Their new mission is to “Ensure the meeting between Kaishu Katsu and Takamori Saigo happens according to history.” Saniwa anticipates that the Time Retrograde will try and interfere, as the meeting is a crucial event that will become a turning point for Japanese history. Izuminokami and Horikawa have thoughts about this era as it is where their formal master used to live. The Time Retrograde Army appears on the last day of the meeting, however, the patrolling Second Unit encounters a powerful opponent, the Ootachi. Meanwhile, Yagen sneaks onto a warship in pursuit of a Roushi who’s not supposed to exist in history. As Yagen tries to stop the warship from bombarding the meeting with cannons, the Time Retrograde Army surrounds him. In this time of great peril, the last Sword Warrior of the Second Unit appears.

In order to steal cargo from the Time Retrograde Army, Izuminokami Kanesada joins the rookie Horikawa Kunihiro at the end of the shogunate period. The two swords complete the mission through their valiant efforts, but what awaits them is a new directive: "At a certain castle town in 1863, the new Time Retrograde Army will appear." Izuminokami and Horikawa prepare to intercept the enemy with this limited information. However, the two swords are unable to fend off the overwhelming number enemies. In their time of crisis, their master "Saniwa" appears.

After defeating the unknown street slasher, the First Unit stays in the Capital instead of immediately returning to the Citadel. At the Captial, Yamanbagiri and his unit are determined to help the citizens recover from the Time Retrograde Army’s assault and the twisted history. Meanwhile, Izuminokami ponders the meaning behind protecting history, and asks the Sword Warriors of the Second Unit to fight with him once more. This time Izuminokami wishes to fight, not at the Master’s directive, but on his own volition. With newfound determination, the Second Unit departs on a new mission.

Horikawa Kunihiro has disappeared from the Second Unit. In order to pursue Ryoma, who left the Satsuma Residence earlier than what was recorded in history, the Second Unit splits up to pursue Ryoma and find Horikawa. Izuminokami and Mutsunokami head to the Satsuma Residence, which is up in flames due to the distortion in history. Horikawa also shows up with a new determination. How will Izuminokami respond to Horikawa…

Unable to stop Horikawa, Izuminokami Kanesada stands there as he walks away. As Izuminokami agonizes over his inability to deny Horikawa’s determination, Saniwa appears in front of him. In order to resolve the regret Izuminokami holds in his heart, Saniwa suggests for them to head to Hakodate – the land where Izuminokami and Horikawa's former master, Toshizou Hijikata drew his last breath. The Time Retrograde Army shows up in Hakodate. With the reinforcement of Yamanbagiri and his unit, Izuminokami will face the Time Retrograde Army and his own regret head on.

With the Second Unit back at the Citadel, the First Unit has now mobilized in Kyoto during 1565. With Yamanbagiri Kunihiro as captain, the First Unit receives a directive to investigate a noise that’s capable of breaking through the wall of time, and stop the Time Retrograde Army from changing the history. In order to discover the Time Retrograde Army’s motives, Yamanbagiri and his unit head to the capital. In this supposedly peaceful town, they hear about a street slasher roaming about that hides his face behind a demon mask. Thinking this slasher might be the key to the potential historical change, the First Unit begins their investigation.

At the Battle of Hakodate, where his former master Toshizou Hijikata would die, Izuminokami runs into Horikawa who is now wearing the emblem of the Shinsengumi. As Izuminokami makes up his mind after a clash of ideals, he heads to Ippongi Kanmon to stop Time Retrograde Army with Mutsunokami and the rest of his comrades. Embracing their mission to protect history, the Sword Warriors of First Unit and Second Unit face off the one thousand Time Retrograde Army troops.

The last Sword Warrior of the Second Unit, Tsurumaru Kuninaga, appears from the time-space distortion onto the warship occupied by the Time Retrograde Army. After saving Yagen, Tsurumaru meets up with Izuminokami and Mutsunokami to defeat the Time Retrograde Army and take back the warship. Meanwhile, as Ootachi overpowers Tonbokiri and Horikawa, they desperately try to protect the meeting from being uninterrupted. Things get worse when another warship bombards Edo and engulfs the town in flames. The Second Unit is now forced into a corner…