Two Flags West is set in the waning days of the Civil War. Colonel Clay Tucker (Joseph Cotten) is one of several Confederate prisoners who agree to fight alongside Union soldiers against the Indians in New Mexico. Tucker's Union commander Kenniston (Jeff Chandler) despises all "Johnny Rebs," holding them responsible for the death of his brother. Kenniston has other problems too; he is deeply in love with his sister-in-law Elena (Linda Darnell), but refuses to express his devotion out of loyalty to his dead sibling. He also hates Indians with a passion, and has endangered the safety of his fort by brutally killing a chief's son. There seems to be only one way for Kenniston to purge the demons within him, and he finds that way during a climactic Indian attack.