In the past, storks were granted the mythic job of manufacturing babies in a factory and transporting them (with the use of beacons) to couples around the world. But one day, a stork named Jasper refused to give up a baby he was assigned to deliver, and destroyed her beacon, effectively orphaning her; an ambitious stork named Hunter took this incident as an opportunity to reinvent the stork delivery business, moving it from delivering babies to express delivery.
In modern times, the storks are now a successful package-delivery corporation called Cornerstore. The orphaned baby, Tulip, is the only human in the whole corporation and serves as janitor. The top delivery stork, a clever but lonely officer named Junior, is to be promoted to company head by Hunter, on one condition: he must get rid of Tulip. But when Junior meets Tulip, he sees that she is a kind and sweet person and instead of firing her he moves her to the now-defunct baby factory and tells her she is in charge of mail.
A young child named Nate Gardner leads a lonely life, with his parents being successful realtors who have no time for him. He therefore decides to write to the Storks, asking for a younger sibling. The letter gets to Tulip and she starts up the baby factory; Junior gets wind of what happened and tries to stop her, but he ends up injuring his wing and a baby is created. With his promotion in jeopardy, he decides to get the baby to its family as quickly and quietly as possible and since he cant fly Tulip has to help him, with a flying machine she made. However, a Cornerstore employee, Pigeon Toady, finds some baby powder and his suspicions are raised. And as Tulip and Junior leave, an elderly Jasper follows them...
Tulip and Junior end up crashing theflying machine. Junior is fed up with everything and leaves Tulip to deliver the baby by foot, but they both get captured separately by a pack of wolves who bring all three to their cave. They manage to escape, and while the Wolf Pack is in pursuit of them they manage to shake them off.
As they journey on, Tulip and Junior start to get closer: Junior admits that he doesnt really care for his promotion as he has no idea what to do as boss, and Tulip confesses that she wants to locate her family just as she is helping the baby to locate its family. Meanwhile, Pigeon Toady has acquired enough evidence to prove Junior is delivering a baby, and he brings it to Hunter so that he can get Juniors promotion. Hunter has the beacon reprogrammed to show a different address.
Junior and Tulip have another encounter with the Wolf Pack at a harbor, but this time Jasper appears and carries away the threesome. He then explains to Tulip that his breakdown was because he wanted to raise her as his own, and that as an apology he has been slowly repairing her beacon over the years. Tulip has carried a piece of the beacon her whole life, and this fragment is the final piece to get her beacon operating again. She is excited about finally being able to see her family, but this upsets Junior into revealing that he was supposed to fire her. Tulip leaves in tears to see her family, having nothing at Cornerstore, while Junior carries on with his delivery.
When Junior delivers the baby, he gets captured by Hunter at the changed address; Hunter fires him and ties him up, and hands over the baby to a flock of penguin assassins. Tulip appears at the address, deciding to help Junior first, and she is able to get them both back to Cornerstore by making an order and then returning it and hiding inside the package. The two arrive at the company while it is having a party; they take advantage of the festivities to find and retrieve the baby from the penguins, but when the baby starts crying they get exposed.
In a moment of despair, the two head back to the baby factory and accidentally restart it, causing a multitude of babies to be created. A horrified Hunter tries to destroy the factory with a crane, but ends up destroying Cornerstore and his machine is thrown from a cliff. Junior rallies all the storks to go back to delivering babies again, and finally completes delivering his baby to the Gardners.
The film ends with Junior and Tulip now partners running the baby factory, and with Tulip finally meeting her family. Jasper takes a family photo, with Tulip inviting Junior to join her.