The story of Senjyushi: The Thousand Noble Musketeers is set in a world ravaged by nuclear war. The survivors are repressed by a tyrannical, world-spanning Empire that deprives the people of their liberty, but although militaries have been banned, a small group of resistance fighters still oppose the Emperor using antique firearms that were preserved as works of art. These men, who have inherited the spirit of their weapons, are known as "Noble Musketeers".