11 episodesFirst aired 17 April 2011
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”.
E1Apr 20111h 46m
Jin examines Saki’s ill mother after learning that she may have beriberi disease due to malnutrition. Ryoma arrives from Kyoto seeking Jin’s help.
E2Apr 201146m
Jin considers the risks of interfering with history by treating an imperial princess with suspected beriberi. An old acquaintance appears before him.
E3May 201146m
Locked away in prison for a crime he didn’t commit, Jin endures harsh conditions and torture. Ryoma and Kyotaro fight to prove his innocence.
E4May 201151m
As the Jinyudo doctors continue trying to create penicillin in powder form, Taki asks Jin for help in treating a noblewoman from an important family.
E5May 201146m
Jin does all he can to help a renowned kabuki actor suffering from severe lead poisoning and limb paralysis to perform on stage one last time.
E6May 201151m
While visiting Nagasaki to teach other doctors about penicillin, Jin catches up with Ryoma but senses that something about him has changed.
E7May 201146m
After receiving a wedding invitation from Nokaze, Saki and Jin go to Yokohama for the occasion. But during the visit, Nokaze wants Jin to examine her.
E8Jun 201146m
As Ryoma fully devotes himself to achieving a return to imperial rule, Jin battles to protect the lives of both a struggling Nokaze and her child.
E9Jun 201146m
As Jin rushes to Kyoto with Saki and Saburi to prevent Ryoma’s assassination, Kyotaro heads for the same destination with a very different mission.
E10Jun 201156m
Jin, Saki and Saburi perform a major surgery to try and save Ryoma’s life. The Jinyudo doctors face charges of teaching how to create fake penicillin.
E11Jun 20111h 32m
Sensing he has little time left, Jin resolves to pass on his entire medical knowledge to the Jinyudo doctors. Kyotaro makes a difficult decision.