In the year 2205, an organization known as the Time Retrograde Army attacks the past in an effort to rewrite history. To counter this threat, the government of time tasks the Saniwa—individuals with the power to awaken spirits within legendary blades—with animating historical swords as warriors called Touken Danshi. In one particular citadel, a group of fifteen Touken Danshi loses their Saniwa in a devastating assault by the Time Retrograde Army. Left adrift and without a master, the warriors hide their citadel in a drifting state to avoid further attacks, sustained only by fragments of a song their master left behind. As spring arrives, they repel another wave of enemies and receive an unexpected communication through a messenger fox named Konnosuke: the government of time has assigned them a covert mission called the Assault Investigation. Tasked with investigating distortions in history, the fifteen swordsmen travel to the Warring States period to begin their dangerous work.

The warriors are split into five units of three. The First Unit is led by the elegant and otherworldly Mikazuki Munechika, joined by the enigmatic Sengo Muramasa and the honest, straightforward Tonbokiri. The Second Unit is commanded by the cultured Kasen Kanesada, accompanied by the protective Ichigo Hitofuri and the energetic Namazuo Tōshirō. The Third Unit is headed by the fiercely loyal Heshikiri Hasebe, with the refined Tomoe Go and the sharp-witted Yagen Tōshirō. The Fourth Unit is led by the unpredictable Tsurumaru Kuninaga, alongside the solitary Ōkurikara and the stylish Shokudaikiri Mitsutada. The Fifth Unit, responsible for the first sortie into the past, is led by the self-conscious Yamanbagiri Kunihiro, with the confident Yamanbagiri Nagayoshi and a mysterious figure named Omokage, a Touken Danshi who appears during the investigation. Omokage carries a large sword and possesses the unusual ability to create mirror images of himself in battle.

As the five units push through fractured battlefields—uncovering five false histories that must be corrected—they realize that the Assault Investigation is not merely a reconnaissance mission. The government's directive seems to treat the warriors as expendable, willing to sacrifice them to restore the proper timeline. During their fights, they encounter a shadowy version of Omokage known as Black Omokage, a missing fragment of Omokage's spirit that was shattered in a previous battle. Black Omokage has become the master of a dream world, using the memory of a historical figure's death as a foundation for that realm, and has allied itself with the Time Retrograde Army. When the citadel itself comes under direct attack, the warriors make a decisive push into the dream world to destroy the threat. Black Omokage tries to trap them in a false version of Edo, but the warriors refuse to abandon their hope of returning to their citadel. In the final confrontation, Omokage absorbs Black Omokage back into himself and severs the dream world from reality, remaining behind to ensure their safe return. The other fifteen warriors return to their drifting citadel, carrying forward both the burden of their mission and the faint hope that their master may one day return.