The story follows a brain surgeon named Minakata Jin who has spent the last two years in anguish, as his fiancee lies in a vegetative state after an operation he performed. One day, he faints at the hospital and awakens to find himself transported back in time to the Edo Period. He is soon attacked by a samurai, but he escapes with the help of a man named Kyotaro. Kyotaro suffers a serious injury to the head while trying to protect him, but Jin manages to save his life despite a lack of proper medical equipment. Because of that, Kyotaro's sister Saki begins taking an interest in Jin and becomes his assistant. Meanwhile, Jin is determined to find a way back to the present.

Two years have passed since the last season. Jin and Saki develop a sweet confectionery that contains medicine for Saki's mother who has a severe case of beriberi. Meanwhile, Ryoma asks Jin to care for Kaishuu Katsu's mentor, Shozan Sakuma. Shozan is in a critical state after being attacked by the Shinsengumi. Jin is reluctant because curing Shozan would mean changing the course of history. However, Shozan tells him that he too is involved in the “present”.