The film concerns Chanticleer, a proud rooster whose singing wakes the sun every morning, or so the other farm animals believe. His singing keeps the other animals happy, and the farm free from downpours, but one morning, he is attacked by a bird sent by the owls. Chanticleer wins the fight but loses his strength to crow, and the sun rises all by itself. Believing him to be a fraud, the other animals ostracize and ridicule Chanticleer, and their insults deeply sadden him. Feeling that he has nothing to do with his crowing, and thus can no longer live on the farm, Chanticleer leaves for New York City. Meanwhile, the animals back on the farm realize that it was a mistake to mock and humiliate Chanticleer into leaving. Without his singing, the sun no longer rises, or as Patou the Dog, leader of the animals put it, "She took a look around, and decided to go back to sleep" (Perhaps because Chanticleer's singing woke the sun up fully, thus no singing, no rising). This brings on the rain, which causes a flood and makes the animals prime targets for their enemy, The Grand Duke of Owls (who the Storm King and Don Karnage are working with).
Doctor Aaron and his crew arrive in the middle of the storm and notice the flood waters which coming from a farm in the countryside and decide to investigate.