The Tweedys run a chicken farm in Yorkshire, England, in the manner of a World War II POW camp. One chicken, Ginger, continually tries to get the chickens to escape from the coop using various plans and contraband obtained through two rats, Nick and Fetcher. They sometimes involve going under the fence. However, Ginger is always caught by Mr. Tweedy and his dogs, and while she is kept in solitary confinement, she comes to realize their only hope of escape is to fly over the coop's fence. One day, Winnie the Pooh, Piglet, Tigger, Rabbit, Eeyore, The Penguins of Madagascar (Skipper, Kowalski, Rico and Private), King Julien, Maurice, Mort, Timon, and Pumbaa arrived to the farm and met Ginger and the other chickens.
Mrs. Tweedy, struggling to keep the farm financially viable on dwindling egg production, decides to convert the farm from egg production to chicken pies, and orders a giant pie-making machine. Mr. Tweedy believes the chickens are plotting a big escape, but Mrs. Tweedy dismisses the idea as paranoia and does so in a rude domineering manner. While the Tweedys await delivery, a Rhode Island Red rooster named Rocky Rhodes appears to "fly" into the coop, though harming his wing on landing. While the other chickens fawn over him, Ginger convinces Rocky to help teach them how to fly much to the surprise of Pooh and the others.
Unable to admit that he cannot actually fly, Rocky plays for time by putting the chickens through seemingly-futile training exercises while he tends to his injured wing. At the same time, the Tweedys provide the chickens with more food in order to make them plumper for their pies. The pie-making machine soon arrives, and as Mr. Tweedy begins construction, Ginger realizes what Mrs. Tweedy's plan is, and that they have very limited time to escape. With the machine completed, Mr. Tweedy attempts to put Ginger through the machine, but she is saved by Rocky and Pooh and the others, and they are able to disable the machine, giving themselves some more time while Mr. Tweedy tends to its repair.
The next day, Ginger and Pooh and the others finds Rocky has fled, leaving behind a part of a poster that explains that he was a circus act, only "flying" over the land after being launched out of a cannon. Ginger and the other chickens lose hope of escape, cumulating in a huge brawl in the mud, until Ginger finds out that Fowler, the farm's aged rooster, was once an honorary member of the Royal Air Force. With Fowler's knowledge, and with the nervous and nerdy Mack's aeronautical engineering, they begin working hastily to create an flying machine. The machine would be pedal-powered by the chickens themselves, in secret from Mr. Tweedy, who has become suspect of the chickens' ingenuity. The craft is completed even as the repairs on the pie-making machine are completed. As Mr. Tweedy attempts to grab the chickens, he is restrained by the attacking chickens and 'hidden' under one of the coops.
The chickens quickly assemble their plane and attempt to take off, despite Mr. Tweedy's attempt to stop them. Mrs. Tweedy hears the commotion outside, and, armed with a hatchet, is able to grab onto a string of lights from the plane before it takes off. Rocky returns to help, and he and Ginger attempt to knock Mrs. Tweedy off, as her weight is too much for the chickens to keep the plane airborne. Ginger tricks Mrs. Tweedy into cutting the light string with her hatchet, causing her to fall right into a vent on the pie-making machine. This causes the machine to explode, in a mushroom cloud of gravy, and destroy their barn and leaving just the door standing. Mr. Tweedy reminds his irate wife that he had warned her and he said "I told you they were organized", Mrs. Tweedy then growls at him, and he then pushes the door on top of her She is Killed by the Door's squahing-ness. Pooh, his friends, Rocky, Ginger, and the other chickens celebrate as they fly off. At the end of the film, the chickens have found themselves a protected bird sanctuary to live in and raise their chicks, with Rocky and Ginger becoming a couple. As the credits roll, Nick and Fetcher discuss the chicken and the egg theory.
In a scene during the credits, Nick and Fetcher continue to argue about the theory but are interupted by Rocky telling them to be a little quiter. They apologise, but silently insult him and criticise him for his supposed "big shot" personality, proclaiming themselves to be the movie's stars.