In May 1944, 5 years since the declaration of World War II, three Royal Homing Pigeon Service war pigeons
are flying across the English Channel with the White Cliffs of Dover in sight, carrying vital messages to Great Britain. Despite the poor weather conditions the pigeons have nearly reached their destination. They are, however, suddenly ambushed and attacked by a German enemy falcon named General Von Talon; two of the pigeons are instantly killed, yet the third, Mercury, is taken as a prisoner of war.
Elsewhere, a small wood pigeon named Valiant is watching an Allied forces propaganda film in his local bar (an overturned rowing boat) in West Nestington along with Hubie, Marina, Rocko, Splatter Pheonix, Petra, Beanie, Timmy, Pikatw, Bonkers, Fawn and Buck. Wing Commander Gutsy, a war hero flies into the bar, informing everyone that signups are scheduled the next day in Trafalgar Square, London. In General Von Talon's lair, Mercury resists interrogation by his captors. Valiant, Hubie and his friends head off to London, bidding Valiant's mother and Felix, the local barman, goodbye. In London, They meet a filthy pigeon named Bugsy, who is wanted by two thugs. In order to escape the wrath of the thugs, he signs up with Valiant, Hubie and the others.
On the way to the training facility, Hubie recieves a call from Winnie the Pooh. Pooh says that he had heard Hubie and his friends were going to recruit and informs that he has sent one of his friends to help train them.
The recruits, Hubie, his friends, Valiant, Bugsy, Lofty, an intellectual red pigeon, and Toughwood and Tailfeather, two strong but dim-witted twin brothers, form Royal Homing Pigeon Service Squad F, and are sent to a recruit training facility where they follow the commands of Sergeant Monty. He declares that they will toughen them up for the RHPS. Hubie and the others are afraid that Monty is the one Pooh had sent, but Monty explains that another bird will be training Hubie's team.
While training begins for the pigeons, Hubie and his friends are reunited with Pooh's friend, Zazu the hornbill. Upon seeing him again, Petra falls instantly in love. Training begins for Hubie's team.
Meanwhile, Von Talon and his henchmen, Cufflingk and Underlingk, try numerous attempts to discover the message's departure location. However Mercury refuses to tell, despite the tortures inflicted upon him, such as irritating him with yodeling music and injecting him with truth serum, before Mercury accidentally reveals the location: Saint-Pierre.
Throughout the training, Valiant develops a crush on Victoria, the camp's nursing dove. Eventually, Gutsy arrives and tells the Sergeant that the recruits need to leave the next morning, despite their training being vastly incomplete. Bugsy, however, decides not to go on the "highly dangerous" mission and flees the camp that night. The next morning, Valiant, Hubie and the others along with Zazu prepare to leave and start to board the plane headed for France, but not before Bugsy shows up at the last second. The journey becomes extremely perilous, as the plane is caught in the midst of dogfight. Their plane sustains heavy damage and the pigeons soon have to bail out, in boxes equipped with parachutes. The pigeons are dropped from the plane; however a technical malfunction causes Gutsy's box to fail to deploy. The plane goes down in an inferno of flames, presumably killing Gutsy in the resulting explosion.
In France, the team meets Charles de Girl and Rollo, two mice from the French Resistance, Mouse Division, the latter being an expert saboteur who lead them to Saint-Pierre, where they receive the message they have been ordered to deliver. They soon come under attack by Von Talon's henchmen, resulting in Bugsy, Zazu and the message being captured. Von Talon takes the message from them and decides to cage them up and eat him later. Valiant, Hubie and the others follow Bugsy and Zazu to the falcon's bunker, where they discover that Gutsy has survived the plane crash. Valiant takes advantage of his small size and sneaks into the bunker with Petra, Beanie and Timmy through the gun barrel, retrieves the message, and frees Bugsy, Zazu and Mercury. Unfortunately, the falcons are alert and give chase. As Gutsy and the others fend off Von Talon's henchmen, Valiant, Zazu and the bird kids fly to London to deliver the message, followed closely by Von Talon.
After a climactic chase by the falcon, Valiant hides in the cottage where he lives, where he is attacked by Von Talon again. With the help of his mother and Felix, Valiant finally defeats the villain by getting a giant hook caught on his medals, leaving him to be beaten senseless by the water wheel. Valiant delivers the message, and upon receiving it, a change of plans is made; they land in Normandy. After receiving the Dickin Medal, Squad F returns to the local bar in West Nestington, where Valiant reunites and shares a kiss with Victoria.
Afterwards, Zazu organizes a boat run by a girl named Maren for Hubie, Marina and their friends and thanks them for their efforts, also telling them that he'll be joining them for a while until he is to return to the Hundred Acre Wood. Before they leave, Zazu then calls Petra forward and surprises her with a kiss on the cheek. A scene is shown after the credits where Petra has remained in a dazed state.