The film starts with Rocky (Zachary Levi) recounting the last adventure. He came upon the farm of the sinister Mrs. Tweedy (Miranda Richardson) before meeting the group of hens led by Ginger (Thandiwe Newton) to escape their fates of becoming food, with Ginger getting rid of Mrs. Tweedy and having her farm destroyed. Since then, they have arrived at a chicken sanctuary, along with their friends like Babs (Jane Horrocks), Bunty (Imelda Staunton), Fowler (David Bradley), and Mac (Lynn Ferguson). In the present, Rocky is telling the story to his and Ginger’s egg, which is starting to hatch. The egg sprouts legs and starts running around, with Ginger and Rocky frantically chasing after it before it lands in a haystack. The egg fully hatches, revealing their daughter, who they name Molly.
Time passes, with Molly (Bella Ramsey) becoming part of the flock and viewing others, like rats Nick and Fetcher (Romesh Ranganathan and Daniel Mays) who bring the hens products from the other side of the lake. She also causes her parents some grief due to her adventurous nature. When she is old enough, Molly gets curious about what is on the other side of their island, but Ginger tells her there is nothing since she is still traumatized by Mrs. Tweedy. Molly also finds one of Rocky’s old posters from when he was a performing rooster, but he tries to keep that part of his life secret from her.
Ginger later sees some trees getting cut down, and, along with Mac and Bunty, they find several trucks for Fun Land Farms featuring happy chickens driving to a specific location. The hens realize there is another chicken farm being set up nearby, and Ginger calls for a meeting with the chickens. They fear that she wants them to go along on another dangerous mission, but they are relieved when she says that they have to hide to avoid detection. However, Molly remains curious and ends up sneaking out while the other chickens are asleep.
The chickens begin to frantically look for Molly until Ginger realizes she made it to the other side of the water, so she and Rocky head out after her themselves, with Bunty, Babs, Mac, and Fowler following close behind. While she is out on her own, Molly runs into another chicken named Frizzle (Josie Sedgwick-Davies), who is pursuing the Fun Land Farms truck. She convinces Molly to join her once the truck stops and they find an opportunity to hop onboard. The other chickens chase after the truck but ultimately lose track of it. Ginger, Rocky, and their friends then discover the Fun Land Farms factory, while Molly and Frizzle end up along with another flock of hens.
Ginger gathers her friends to break into the facility to save Molly. Rocky attempts a heroic entrance but gets caught in a bunch of the security traps that zap him with electricity before me somewhat successfully manages to get across the wall into the factory. The hens then go to Nick and Fetcher for help in breaking in. They are initially reluctant to help until Ginger informs them Molly is in danger. The chickens use a cake to sneak in past the guards after creating other diversions to make their way in. Rocky, Nick and Fetcher end up nearly getting burned by the furnace, but they use an umbrella to propel themselves to safety.
Meanwhile, Molly and Frizzle appear to be enjoying their time in the facility, until Molly notices the other hens they came with have collars around their necks while they seem too happy and oblivious to what’s going on around them. They are found by Dr. Fry (Nick Mohammed), who designed the facility and all the mechanisms around the hens. He gets a collar for Frizzle, which leaves her brainwashed as well. Molly realizes something is not right and starts to make her own attempt to escape.
Dr. Fry greets Reginald Smith (Peter Serafinowicz), the owner of Sir-Eat-A-Lot family restaurants. Fry shows him a video on how the chickens there are made to be happy as they end up getting turned into food. Molly and Ginger wind up in the room at the same time, just as a familiar voice speaks to the men in the room. Ginger reacts with horror as she sees none other than Mrs. Tweedy coming down the stairs. She has remarried to Dr. Fry (for his money, land, and intelligence) and demonstrates by having one of the mind-controlled hens gleefully walk into the machine, turning her into ready-made chicken nuggets set for distribution. Reginald samples one and likes it, agreeing to sell Mrs. Tweedy’s chicken.
Just as Mrs. Tweedy finishes her deal, she recognizes Ginger and suddenly goes into revenge mode. She gets Fry to come in and prep Ginger to become the next batch of nuggets. Babs, Mac, and Bunty hack into the cameras and are all horrified (along with Rocky, Nick and Fetcher) to see Mrs. Tweedy back again. Rocky and the rats cut the wires to prevent Ginger from getting brainwashed before Molly frees her mother. The group rejoins and tries to make their escape, but they all end up trapped in a corn silo with seemingly no way out. When Mrs. Tweedy finds out, she turns on the grinder to kill the chickens (and rats). Molly blames herself for getting them all into this mess, until they realize they can make popcorn (something Rocky earlier showed Molly) using fireworks and Mac’s glasses reflecting sunlight to boost themselves out of the silo to freedom.
The group rejoins Fowler on the roof before they attempt to ride a zipline down back to freedom. However, Molly wants to rescue Frizzle and the other hens, and Ginger doesn’t think twice to help her daughter. The others follow suit for the rescue mission. Mrs. Tweedy prepares to ready up all the hens for the nugget process as Reginald sends trucks to pick them up. She catches the chickens sneaking back in, so she activates the collars and has the hens walk toward the grinder. The group tries to hold them back from walking while Ginger tries to steal Mrs. Tweedy’s remote. As the hens edge closer to their deaths, Mrs. Tweedy catches Molly and threatens to kill her unless Ginger gives up the remote. Rocky swings in to save his daughter, leaving all three hanging over the edge. Mrs. Tweedy prepares to kill them all until the axe Rocky swung in on whacks her in the face, sending her falling into her grinder as Ginger turns off the hens’ collars.
The heroes gather all the other hens into one of Reginald’s trucks, but Mrs. Tweedy emerges fried and coated in breadcrumbs. She grabs an axe and chases after the group before Fowler knocks her into a moat while the truck flies over a ramp. Fry comes out to warn Mrs. Tweedy that the processor is overheating, just as she gets zapped by duck drones in the moat. Fun Land Farms then explodes and crumbles while the heroes return home.
The chickens expand their sanctuary to include the newly rescued hens. Molly and Frizzle return after doing reconnaissance and inform Ginger and Rocky that there is another chicken farm operating nearby. Ginger and her friends and family band together for yet another rescue mission.