Bob Morlock is an interstellar businessman who also happens to be the oldest living being in the world. Feeling that his time to depart has finally come, Morlock wishes to go back in time to the very beginning, in order to witness the Big Bang and the creation of the universe. His company Kanary has a clone-constructing department, which promptly produces the fearless Clone Consortium Commander Blood, who must navigate his ultra-modern ship, the Ark, in order to fulfill the wishes of the eccentric boss.

Commander Blood is a follow-up to Captain Blood. Like its predecessor, it is an open-ended, space- (and time-) travelling adventure game that relies on complex communication system with the various creatures inhabiting the universe. The game utilizes pre-rendered scenes and animated sequences, as well as animation technique involving live action puppeteering in front of a chroma key screen.