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.

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.

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.

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…