On Bird Island, an island inhabited by flightless birds, the reclusive Red is sentenced to an anger management class after his temper causes a “premature hatching” of a customer’s egg. Resentful, Red avoids getting to know his classmates Chuck, Bomb, and Terence, as well as the class’s instructor Matilda. One day, a boat docks at the island’s shore containing green-colored pigs, and their captain Leonard, who claim to be peaceful explorers bringing offerings of friendship. The pigs are accepted on the island and introduce the birds to innovative technologies such as slingshots and helium balloons.
More pigs arrive and seemingly adjust to the bird’s society, but Red soon becomes suspicious of their motives, as they slowly overwhelm the island. He recruits Chuck and Bomb to help him find Mighty Eagle, a giant bald eagle said to be the protector of the island, and the only bird that can fly, but who has not been seen for many years. They find Mighty Eagle on top of Bird Mountain, but he is now overweight, self-absorbed, and largely in retirement. Looking through the Mighty Eagle’s binoculars, Red’s group sees the pigs planting explosives around the island while the birds are at a rave party. They realize the party was actually a cover for their plan to steal the birds’ eggs. Red, Bomb, and Chuck attempt to warn the other birds and stop the pigs, but they arrive too late as the pigs escape with the eggs and their explosives destroy the village. When the birds realize what happened, they apologize to Red for not believing him, and the forgiving red bird rallies them to let their anger loose and retrieve their eggs.
The birds construct a boat and sail to Piggy Island, where they find the pigs living in a walled city and Leonard, who is actually revealed to be King Mudbeard, the king of Piggy Island. Deducing the eggs are most likely in the castle at the center of the city, the birds attack and defeat the pigs by firing themselves over the walls using their gifted giant slingshot. However, when Terrence attempts to launch himself into the city, he accidentally snaps the slingshot in half after pulling himself too far back. Meanwhile, Red, Chuck, and Bomb make it to the castle and find the eggs in a boiler room, where the pigs plan to cook and eat them. Mighty Eagle arrives, having watched these events through his binoculars and had a change of heart, and carries the eggs out of the castle. While the birds escape, one egg falls out and rolls back into the castle. Red battles Leonard and retrieves the egg, escaping as the pigs’ reserve of explosives blow up and destroys Piggy Island. Red reunites with the other birds as the rescued egg hatches, revealing three little blue birds (The Blues), and is declared a hero. He, Chuck, and Bomb are approached by Mighty Eagle, who claims that he wasn’t lazy but instead deliberately made the birds lose faith in him so they could find faith in themselves. Returning to Bird Island, the birds rebuild Red’s house, which had been moved by Red near the edge of the island and was gradually destroyed whenever a boat full of pigs had arrived, in the middle of their village. All of the birds that have hatched sing a song to Red to thank him and enshrine him as a legendary hero, and Red lets Chuck and Bomb move in with him.
During the end credits, the pigs are revealed to survive Piggy Island’s destruction, as King Mudbeard begins to make a new plan to steal the eggs. In a mid-credits scene, the three blue birds that Red rescued use the rebuilt slingshot to launch themselves out to sea.