After the death of Yoritomo in 1199, Sanetomo's grandfather and ShikkenHōjō Tokimasa usurped the political and military power of the Shogunate, relegating the position and title of Sei-i Taishōgun, or shōgun, to a figurehead. Through hereditary succession, Sanetomo's older brother Yoriie became Sei-i Taishōgun in 1202, only to be stripped of the title a year later and put under house arrest for plotting against the Hōjō clan. This was presumably to keep the shōgun a child and thus needing a regent to make decisions in his place. Shortly thereafter in 1203, Sanetomo became head of the Minamoto clan and was appointed Sei-i Taishōgun. In the next year, 1204, Yoriie was assassinated by the Hōjō. Sanetomo was never more than a puppet for his mother Hōjō Masako, who used him as a pawn in her war with her father Tokimasa; Tokimasa tried to depose his grandson a number of times, beginning in 1205, causing Sanetomo to fear for his life thereafter.
''Waka'' poet
Sanetomo, understanding his own powerlessness and not wanting to meet the same fate as his brother, put his time and energy into writing waka poetry and gaining posts within the powerless but honorary imperial court. Sanetomo was a talented poet, writing over 700 poems between the age 17 and 22 while he was tutored by Fujiwara no Teika. He published his private waka collectionKinkai Wakashū, even having one of his tanka included in the anthology Ogura Hyakunin Isshu, a collection of Japanese poems of the Heian and early Kamakura periods. Sanetomo reached the third highest post of the imperial court, Udaijin in 1218. Eventually, Sanetomo lapsed into inactivity and despair, plagued by fear of assassination and tormented by his chronic alcoholism.
Death
Under heavy snow on the evening of February 13, 1219, Sanetomo was coming down from the Senior Shrine at Tsurugaoka Hachiman-gū after participating in a ceremony celebrating his nomination to Udaijin. His nephew Kugyō came out from beside the stonestairway of the shrine, then suddenly assassinated him. For his act, he was himself beheaded a few hours later, thus bringing the Seiwa Genjiline of the Minamoto clan and their rule in Kamakura to a sudden end. Minamoto no Sanetomo was succeeded by Kujō Yoritsune as fourth shōgun of the Kamakura shogunate.