For ages, storks have delivered babies all around the world. No matter what they had to face, they did their job with no complaints. In the present day, however, Stork Mountain has become home to Cornerstore.com, and storks now deliver packaged goods to customers.
Junior (Andy Samberg) is the top delivery stork, having just completed his one-millionth delivery. He is called to meet with the boss, Hunter (Kelsey Grammer). Hunter is up for a big promotion following the annual StorkCon, and he is set to move Junior up to Vice President of the company. Junior is excited, but first, Hunter orders him to fire Tulip (Katie Crown), the only human on Stork Mountain. When Tulip was a baby, her stork, Jasper (Danny Trejo), tried to take her for himself, and he accidentally broke her beacon, leaving the storks unable to find her home. Now that Tulip is turning 18, Hunter thinks it's time she go out into the human world.
Junior heads over to talk to Tulip, who has created jetpacks to help a quail, chicken, and emu achieve their dreams of flying. One of the jetpacks malfunctions and starts a fire that wrecks part of the factory. Tulip starts crying because she thinks she's a screw-up, and Junior is unable to bring himself to fire her, so he has her move to the letters department where old letters to the storks are stored. Tulip quickly gets bored and pretends to be other people to entertain herself.
Somewhere far away, a young boy named Nate Gardner (Anton Starkman) is playing a game where he pretends to be part of a ninja squad. He expects his parents Henry and Sarah (Ty Burell and Jennifer Aniston) to play, but they are very preoccupied with their careers in real estate. Nate then decides he wants a little brother, but his parents don't know how to explain to him where babies come from. Nate finds a pamphlet in his attic that explains the stork delivery system, so he writes a letter to the storks as his parents to request a younger brother with ninja skills.
The letter makes its way to the factory and into Tulip's possession. She mistakenly slips it into the baby-making machine. Junior watches this in Hunter's office through security cameras. He rushes to the machine room to stop it, having to slip his wing into a dangerous mechanism to hit the emergency shut-off button. Unfortunately, a baby has already been created. Junior decides he has to deliver the baby before Monday when StorkCon happens so that his promotion chances don't get ruined. He then finds a plane that Tulip built for apparently delivering packages for Cornerstore. They take the plane with them and head out for the delivery.
One of Junior's coworkers, Pigeon Toady (Stephen Kramer Glickman), finds BABY POWDAH in the factory. He takes his own little flying device to head out and find Junior, Tulip, and the baby.
Nate starts to gather items to build a landing pad for the storks to deliver the baby. Henry steps outside to see this and agrees to help for a few minutes. Time passes and he's having so much fun with his son that he doesn't care. Sarah sees the two of them and tries to get them to stop, but Henry convinces her that they have to spend as much time with Nate as they possibly can. Sarah decides to join the fun by smashing the chimney.
As Junior and Tulip fly on, they hear that the baby is upset. Tulip's maternal instincts kick in and she goes to take care of the baby, leaving the plane without a pilot. Junior forgets to turn on the autopilot, so the plane crashes near an icy area. Junior and Tulip argue, and he heads out on his own. He is ambushed by a pack of wolves that knock him unconscious.
Junior wakes up hanging upside down next to Tulip, who is still mad at him. The wolves then gather as the Alpha and Beta (Keegan-Michael Key and Jordan Peele) surround the baby. They plan to eat her, but they start licking her and fall in love with her. The baby starts laughing when Tulip hits Junior, and the wolves are all mesmerized by the baby's adorable laughter. Tulip convinces the wolves to cut them loose so she can hit Junior more. She grabs a large branch and whacks the Alpha over the head, allowing her and Junior to run with the baby. The pack chases after them, taking on many crazy forms like a bridge, boat, and submarine to catch up. Junior makes it back to the plane, but Tulip nearly falls into a crack in the ice. Junior runs to go save her. They push the plane down into the water since it has a raft to let it float. The wolves try to form a plane, but they fall since they can't fly.
The three are now floating along the river. Junior gets nervous when Tulip keeps asking him why he wants to be boss and the whole stork-baby relationship, so he stabs the raft and forces them to take shelter in a nearby cave. Tulip braids Junior's feathers, and the two bond over their jobs and goals. Tulip admits she built the plane to find her family, and she kept one piece of her beacon in case she could manage to succeed. Junior assures her that she will find them. The two try to go to sleep but are both kept awake by the baby. They do what they must to get her to fall asleep.
The three continue their journey, while Toady continues to follow them, and the Gardners continue bonding as they build their landing pad. Toady eventually gets enough information to bring back to Hunter, who plans to have Junior and Tulip return the baby. Toady changes the beacon address from the Gardner home to Cornerstore HQ.
Junior and Tulip find a boat that they think will help them get to the baby's home. They try to go by undetected, but the baby starts making crying sounds. She reaches her arms out for Junior, so Tulip hands her over before she wails. Junior holds the baby and finds himself growing attached to her. They head toward the boat but are then found by the wolf pack again. When it looks like they're goners, the three are rescued by Jasper. He brings them onto the boat and explains that he fell in love with Tulip when she was a baby, and he felt so bad about breaking the beacon that he spent the last few years recovering all the pieces. Tulip pulls out the last piece, repairing the beacon. Tulip gets excited since she can finally meet her family, but Junior crushes her happiness when he admits that he was supposed to fire Tulip for being a screw-up. Tulip tearfully leaves with Jasper while Junior decides to bring the baby home.
Jasper brings Tulip to her family's home, but she decides to go back for the baby.
Junior arrives at the location where the beacon has brought him. At the same time, the Gardners hear a knock on the door, and they think it's the stork. It's actually a police officer with a cease-and-desist to tell the Gardners they need to take down their pad because it's unsafe. Henry and Sarah tell Nate the truth about how storks don't deliver babies anymore and that they just wanted to spend time with him. Nate sadly takes down the lights he put up to attract the storks. Meanwhile, Junior realizes he's walked into a trap as Hunter and Toady take the baby away from him with Hunter's penguin minions. After they leave, Tulip arrives and orders a package and has it returned to Cornerstore with her and Junior stowed away in the box.
The two have arrived in the middle of StorkCon as Hunter is giving a presentation. They sneak away in a costume as they find the penguins trying to take the baby away. Since the baby is asleep, Junior and Tulip fight the penguins while being as quiet as possible. Once they recover the baby, they accidentally draw attention to themselves from Hunter and the other storks. They chase after the three and are lead into the baby-making machine room. Hunter tries to get the baby away from Junior by promising he can still keep his job, but Junior instead grabs the hose to the letter room and stuffs the machine with hundreds of letters, mass-producing babies. The storks rush to grab the babies. Hunter takes control of a giant robot to try and destroy the machine, but his control pad is being messed with by the baby. The robot gets pushed out of the factory and gets caught on wires that start to pull the factory off the mountain. Hunter plummets to his doom, but not before using the robot claw to pull Junior, Tulip, and the baby down with him. Junior then manages to fly himself, Tulip, and the baby back to the top.
With a huge number of babies among them, Junior assumes command of the storks and says that baby-delivering is what they were all meant to do. The storks (and a reformed Toady) agree, and they all head out around the world to deliver babies to couples of all kinds. Junior, Tulip, and Jasper bring their baby to the Gardners as Nate shines a light to bring them closer. Junior hands the baby over to them, and he suddenly has a vision of the baby as she grows from an infant to a young woman. He says goodbye to the baby and flies away with Tulip and Jasper. Nate is at first disappointed that he got a sister instead of a brother, but he is pleased when the baby shows off her ninja skills as he requested.
Tulip is brought to her home with all the birds (and the wolves) right behind her. She rings the bell and sees a large family with puffy red hair like hers. They know who she is, and they all hug her. They gather around for a group photo, and Tulip invites Junior to join them.
*CUT TO THE CHASE*
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Storks now deliver packaged goods instead of babies, but that changes when Tulip accidentally creates a baby. She and Junior must deliver the baby to her family before Junior loses his shot at a promotion. They are pursued by Pigeon Toady. Meanwhile, Nate Gardner wants a little brother to play with, so he and his parents build a pad for the storks to deliver the baby.
Hunter takes the baby away from Junior to protect his feathers, but he is eventually defeated and falls to his doom along with the whole factory.
The storks go back to baby-delivering, Nate gets his sibling, Junior is now boss, and Tulip finally finds her family.
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