After the fall of the Taira in Book 11, there a period of peace until a violent earthquake strikes which causes significant damage to the imperial capital, including the destruction of six great temples, as well as palace buildings, shrines and many houses. The sun is covered, and the sky turns black due to smoke and people are struck with fear. The destruction of the earthquake extends across Japan, causing the earth to split open, mountains to fall, and floods to rise. People believe this was caused by the rage of angry ghosts from the drowning of the emperor and the parading of heads of the Heike.
We learn that Mongaku, who had goaded Yoritomo into starting the war by presenting him with his father’s skull had used any old skull to urge the now-hegemon to action. Now, he brings the real skull to Kamakura. It had been taken down from the prison gate where it had been hung after the Heiji rebellion by an indigo dyer favored by Yoshitomo. The dyer had kept it in the hopes that Yoritomo would rise to avenge his father. Yoritomo receives the skull with great solemnity and orders construction of a temple to house it. Yoshitomo is posthumously raised in rank.
Tokitada, a courtier with long-standing close ties to Go-Shirakawa and the Taira, is sent into exile. We are reminded of his past deeds, including the branding of one of Go-Shirakawa’s envoys sent to the Taira camp in Yashima (Book 10, episode 4).
Yoritomo, fearful of Yoshitsune’s popularity and alarmed by rumors of his ambitions, sends Tosabō Shōshun to assassinate Yoshitsune. Tosabō travels to the capital in the guise of a pilgrim, but Yoshitsune divines his true intentions immediately. Tosabō swears oaths that he is not there to kill Yoshitsune. During the night, Yoshitsune’s faithful lover Shizuka confirms that a night attack is on the way. Yoshitsune meets Tosabō and his men in full armor, killing all but Tosabō who escapes to Kurama but is quickly apprehended. Yoshitsune praises his loyalty to Yoritomo and offers to send him back to Kamakura, but Tosabō says he would rather die. Yoshitsune has him beheaded, but all praise his bravery.
Yoritomo now tries to send Noriyori to kill Yoshitsune. Noriyori is reluctant, Yoritomo now suspects him, too, and has him executed. Yoritomo next sends his father-in-law, Hōjō Tokimasa, to punish Yoshitsune. Yoshitsune plans to flee to Kyushu and asks Go-Shirakawa for a letter of support, which he is granted. He is unsuccessful in sailing to Kyushu, however, and ends up in Yoshino. People turn against him, perhaps out of fear of Yoritomo. He is chased to the far north. Tokimasa arrives in the capital, and now Go-Shirakawa issues a call for the suppression of Yoshitsune.
Yoritomo applies for the position of constable over all Japan, which is eventually approved. Yoritomo assigned a ward to each province and communicated with the court through the Yoshida grand chancellor Tsunefusa. Tsuenefusa was known for his “strike fairness,” once aided the Heike in confining the cloistered emperor to the Toba Mansion, and rose swiftly through the ranks to become the Dazaifu deputy. Yoritomo asks Go-Shirakawa to appoint him constable over all Japan, and Go-Shirakawa feels compelled to reply. Yoritomo comes to rely on Tsunefusa, the Yoshida Grand Counselor, as his go-between to the senior nobles.
Tokimasa is rounding up any boy possibly of Taira blood and executing him. Rokudai has been in hiding and is now 12, but he is discovered by Tokimasa and taken into custody at Rokuhara, in Kyoto. Rokudai’s nurse learns of Mongaku of Takao and urges him to make Rokudai his disciple. Mongaku promises to get a reprieve from Yoritomo, and says he will return with the reprieve in 20 days. He leaves for Kamakura, but does not return in 20 days. Tokimasa starts down the Tōkaidō with Rokudai, but they do not encounter Mongaku. Tokimasa prepares to execute Rokudai, but Mongaku suddenly appears with the reprieve, thus freeing Rokudai.
Rokudai rushes to Daikakuji, but can’t find his family, since they are on pilgrimage to Hase. Saitōroku travels to Hase, tells Rokudai’s mother of the reprieve, and they are united at Daikakuji. She urges Mongaku to make Rokudai a monk, but Mongaku is reluctant; he does return with him to Takao, however, and offers support to Rokudai’s mother. Meanwhile, Yoritomo has ordered the execution of two other former allies, his uncle Yukiie and Yoshinori. Yukiie is eventually found in Izumi, where he is captured by the fighting monk Hachibō. Tokimasa orders Yukiie’s execution. The retainer Heiroku chases down Yoshinori, eventually finding him having committed suicide in Sendo. Both Hachibō and Heiroku are exiled for killing senior commanders, but are eventually pardoned and rewarded with landholdings for eliminating Yoritomo’s rivals.
This episode recounts the various Taira partisans killed by Yoritomo’s order. It ends with the beheading, finally, of Rokudai, after Yoritomo has died and Mongaku has been exiled for attempting to dethrone Go-Toba. Although the world was ostensibly quieted with the conclusion of the war (Book 11), it is clear that unrest continued, and the tale ends with the note: "So at last ended the Heike line."