There is a reference to the anime Outlaw Star (1998) where Mugen draws his sword closely at a thug's neck while he pulls out his gun. Gene encounters a similar situation in the "The Seven Emerge."
This episode draws from the actual Catholic missionary movement that came from Spain to Japan in the 17th century. For a more solemn, brutal version of the basis, check out Shusaku Endo's novel, Silence, or the Scorsese film adaption of the same name.