After the events of Season 1, with the assassination of Serizawa and his factions, the hierarchy and organizational structure of Shinsengumi began to change.
Kondo became the sole leader of Shinsengumi, with Hijikata becoming the vice-commander. Fast forward to the Ikedaya incident in 1864, in which the Shinsengumi prevented the burning of Kyoto.
The event made the Shinsengumi famous and known throughout Japan. However, the Shinsengumi will soon faces more tragedy as their story continues in this second season.