The Tweedys are a middle-aged couple who run their chicken farm somewhere in Yorkshire, England. Mrs. Tweedy serves as the genius, while Mr. Tweedy is rather slow and insane, but handles his manual work industriously. The coop is run in the style of a World War II POW camp, with the chickens accountable for the number of eggs they lay daily. Thomas, Twilight and the others (along with Dumbo, Timothy Q. Mouse, Jim Crow and his Brothers) are somehow joined in the farm and they all are being held prisoners along with the other chickens. One chicken, whose name is Ginger (who is a close friend of Thomas, Twilight, Dumbo and the others), who is often treated as the chickens’ leader, has attempted numerous plans to flee the coop, aided by contraband smuggled in by two rats and Timothy Q. Mouse’s uncles, Nick and Fetcher. However, Ginger is routinely captured by Mr. Tweedy and his dogs, and is thrown into a coal bin for solitary confinement numerous times during the opening credits. Ginger is finally released from the coal bin just in time for roll call the next day. Mrs. Tweedy finds on her clipboard that a chicken named Edwina had not laid any eggs that day. With that, Mrs. Tweedy grabs Edwina and takes her to the chop. Mrs. Tweedy beheads Edwina with a hatchet and cooks her for dinner. Ginger becomes increasingly desperate to find a plan of escape which will work, faces problems with Nick and Fetcher, who are tired of being paid with chicken feed and want their own eggs instead.
 
Meanwhile, Mrs. Tweedy realizes that the couple’s farm is failing, and reads a catalogue on an ambiguous method of increasing profits at the couple’s farm. Ginger, realizing something is wrong, attempt to convince herself, our heroes and the other chickens to speed up their efforts to escape. However, Ginger soon comes to the conclusion that the only escape route is to go over the fence, something Ginger and the other chickens cannot do. Rainbow Dash suggests that she, Fluttershy, Heckle, Jeckle, Dumbo and the crows can carry everyone over the fence, but she realizes that . Later that same night, as Ginger sits outside with Thomas, Twilight and the others, they see a Rhode Island Red cockerel that seemingly flies over the fence and accidentally crashes into the coop. The other chickens fawn over the new arrival, who introduces himself as Rocky and Thomas, Twilight, Dumbo and the others introduce themselves to him, while Ginger finds the first half of a poster with a picture of Rocky on it; showing it to the other chickens and explaining how Rocky came in, Ginger claims that Rocky can fly much to our heroes’ surprise. Upon discovering that Rocky is from a circus, Ginger agrees to hide Rocky from his owners if he teaches them and our heroes how to fly. Rocky reluctantly agrees, but due to injuring his wing as a result of his landing, he cannot show them immediately. Instead, Rocky puts Ginger, the other chickens, Thomas, Twilight, Dumbo and the others through a set of exercises that seem to have no purpose while assuring them that everyone are making progress.
 
Meanwhile, a large pie-making machine arrives, which Mr. Tweedy begins assembling. At the same time, Mrs. Tweedy orders all food rations doubled. Ginger proclaims that their intent is to fatten them up, and then kill them, only for Rocky to drag her off. The two of them argue, Rocky claiming that Ginger’s honesty will demoralize the chickens, and Ginger refusing to lie to the other hens. Discovering that the chickens have gone into depression following Ginger’s announcement, Rocky organizes a party by using a radio obtained by Nick and Fetcher, and he and Ginger grow closer whilst dancing. During the party, Rocky’s arm is shown to have healed.
 
Once the pie machine is complete, the Tweedys kidnap Ginger for its first test. Rocky, Thomas, Twilight, Dumbo and the others follow Ginger into the machine and eventually rescue her by damaging the machine and giving them all and Ginger more time to work on their escape. Fowler, an older cockerel who has been doubting of Rocky’s acts, gives Rocky his respect for rescuing Ginger and his old Royal Air Force (RAF) badge in tribute. Rocky decides to flee the farm the next day, leaving behind Fowler’s medal and the second half of his poster, showing that he was actually a stunt cockerel, only the word “flying” by being shot out of a cannon. This revelation saddens Thomas, Twilight, Dumbo and the others and outrages the other chickens and a fight soon breaks out as morale falls. When Fowler arrives to try and restore order, he begins talking of his days in the RAF, leading Ginger to realize that she, our heroes and the other chickens can build their plane made from Fowler’s pictures and personal recollections. Supplied by Nick and Fetcher, the chickens and our heroes race against time to assemble their plane as the Tweedys work to repair their pie machine.
 
The chickens and our heroes finally finish their plane just as Mr. Tweedy completes all the repairs of the pie machine and enters the coop to grab all the chickens. However, the chickens launch an open revolt by tying up and gagging Mr. Tweedy and readying their plane. As the chickens and our heroes prepare to depart, Mr. Tweedy ends up freeing himself and knocks down the ramp used to get the chickens’ plane airborne. Ginger jumps down while Fowler turns the plane around, which knocks Mr. Tweedy unconscious. As Ginger struggles to lift the ramp, Mrs. Tweedy arrives and attempt to kill Ginger with her used hatchet. However, Rocky, having had a change of heart, jumps over the fence aboard his tricycle and hits Mrs. Tweedy in her face, briefly knocking her senseless.
 
Rocky and Ginger finally grab onto the string of lights caught on the plane’s landing gear as the plane departs (with Rainbow Dash, Fluttershy, Heckle, Jeckle, Dumbo, Timothy and the five crows flying close behind), but Mrs. Tweedy soon awakens and also grabs the lights that weighs down the chickens’ plane. Ginger heads down the string to cut it, but accidentally loses her scissors. Realizing what is the only way left to cut the lights, Ginger manages to trick Mrs. Tweedy by using the hatchet to sever the string, which causes Mrs. Tweedy to fall, crash into the pie machine, and plugging her into the safety valve. This causes the pie machine to build-up pressure and explode in a mushroom cloud of gravy, destroying the barn, and covering the entire farm with gravy, leaving only just the barn door standing. Thomas, Twilight, Dumbo, all the others and the chickens continue to fly to freedom as Mr. Tweedy reminds Mrs. Tweedy: “I told you they was organized” before he pushes the door on top of Mrs. Tweedy before she can lash on him.
 
In the epilogue, the chickens find their idyllic setting in a bird sanctuary, where they can live in comfort and raise their new chicks with Thomas, Twilight, Dumbo and the others happily watching. Rocky and Ginger, having fallen in love with each other, become a couple. Meanwhile, Nick and Fetcher discuss their plans of starting their own chicken farm, so they can have all the eggs they could eat. However, Nick and Fetcher ends up arguing with each other over whether the chicken or the egg came first. Their argument ultimately continues during the closing credits and even involves Rocky and Thomas breaking it up during the post-credits scene.