It is the American Civil War, and the Stooges enlist in the service. Moe and Larry accidentally join the Union Army, while Curly manages to correctly sign up with the Confederate. Before the error can be corrected, several Union soldiers order Moe and Larry to lock up their "prisoner." A few moments later, a Confederate general sees Curly being released and, upon seeing Moe and Larry, thinks he has captured two Union soldiers. This mix up goes back and forth several times, until Moe and Larry finally find Confederate uniforms, only to be caught in Union army headquarters. They eventually escape by performing minstrel song-and-dance routine in blackface, with Curly playing a Mammy-type character and Larry strumming a banjo.
They sing "Dixie" with parody lyrics:
"Way down south in New York City The cotton grows on the trees so pretty On the trees On the trees In the South South Brooklyn!"
Uncivil War Birds was produced after Curly Howard suffered a mild stroke. As a result, his performance was marred by slurred speech, and slower timing. In addition, Moe Howard and Larry Fine are paired together and given the lion's share of the film's dialogue.