The story focuses on the main character Sayori, who is a modern high school girl. She finds a mysterious pendant while out helping with an archeological dig (she's in the high school history club, so she is forced to attend), and later has a strange dream—it seems that the scene is from about a hundred and fifty years ago, during the last days of the samurai, and she sees Hatsuhime, princess of the Mochizuke clan, assassinated!
It gets even more strange when the scene changes, and Sayori realizes that she's in Hatsuhime's body; that she has somehow seen how things were, and the situation has somehow "reset", giving her the chance to avert the princess's terrible fate.
Source: Wikipedia, "[en.wikipedia.org/wiki/Yo-Jin-Bo Yo-Jin-Bo]", available under the CC-BY-SA License.