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In the U.S. Army intelligence office, bumbling lieutenant Peter Stirling receives a coded message from his friend, Francis, a talking mule.  The note urges Pete to hurry to the Coronado, California naval base, where Francis is about to be sold as surplus.  Pete rushes to the train station, but before he can board, nurse Betsy Donevan mistakes him for her shell-shocked brother, Navy boatswain Slicker Donevan.  She tries to forcibly remove his uniform so he will not get into trouble for impersonating an Army officer.  Finally she realizes that Pete is not Slicker but merely his mirror image.

The confusion continues in Coronado, where Slicker's best friend Murph sees Pete and quickly assembles his buddies, Jonesy, Tony and Rick, to "save" Slicker.  Later, while Pete bids to buy Francis at auction, the real Slicker returns to his base, where his friends inform him that they just saw him dressed in an Army uniform.  Slicker heads to the auction, and there steals Pete's wallet when he puts it down.  When Pete then cannot pay for his bid, a disgusted Francis instructs him to pawn his bags.  Outside the pawnshop, however, Slicker calls the military police and urges them to arrest his double, supposedly to keep him out of trouble.  As soon as the MPs strip Pete of his uniform, Slicker steals it and assumes Pete's identity.

At the Navy base, Commander Hutch, who considers Slicker to be his star boatswain and a naval hero, immediately places Pete in the psychiatric ward.  There, Pete learns that Slicker is also a famed ladies' man, when each nurse kisses him warmly.  After days of failing to convince the doctors that he is not Slicker, Pete sneaks into the testing site where Francis is being used for transportation experiments.  The mule advises him to pretend he is Slicker in order to obtain a release from the hospital.

Soon, Pete is under the watch of Slicker's four buddies, and, upon seeing Nancy again, finds it difficult to act as if she is his sister.  On his first outing as boatswain, Pete capsizes the boat, but when he revives, he discovers that because the steering was faulty, he is now being lauded as a genius for having steered the boat close to the shore.  His pleasure, however, is soon cut short by the news that he is to enter a boxing match that evening with the Navy's champion fighter.  Pete races to consult Francis, who has grown fond of his cushy pen and informs Pete that in one week the Army will be joining the Navy for tactical maneuvers, at which point Pete will be able to argue his case to the Army commander.  Pete names Francis his mascot for the fight, and as soon as it begins, the mule tries to help him by greasing his opponent's shoes and sitting on the starter bell.  Despite the attempts, Pete is quickly knocked out, and although he feels humiliated, he is delighted by the continued loyalty of Slicker's four friends.  Suddenly realizing that the Navy is as important as the Army, Pete throws himself into studying Naval rules, with Francis as his tutor, and excels at his duties during the following week's intensive training.

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One day, when Pete is visiting Francis at the testing site, Slicker arrives and, nonplussed to hear Francis talk, gratuitously offers to turn himself in.  Although Pete agrees, Francis convinces him that it was a harmless prank and he should take the opportunity to return to the Army.  Pete, jealous of Francis' quick attachment to Slicker, heads to the bus station, but is once again stopped, stripped and returned to Coronado by MPs.  In the barracks, Slicker provides Pete with Navy clothes and helps him sneak out, but Pete, in his hurry to avoid Hutch, mistakenly climbs into the barracks again through a window.  Hutch enters, causing Slicker to hide in a duffle bag, and when the bag falls out of a truck, he hits his head.

He wakes in the hospital, attended to by Nancy, who informs him that Pete, at the risk of being court-martialed, has taken Slicker's place as head boatswain in the Army/Navy maneuvers.  Pete, Murph and Jonesy are placed in a special amphibious "duck" boat, which must reach the shore before the supply ship.  When the good-luck horseshoe in Pete's pocket renders the compass useless, however, he inadvertently steers the "duck" ten miles out of position forcing the sailors to drive it over land to the correct beach.  On the way, Jonesy climbs onto a truck to ascertain their position and, when the truck turns a corner, tells them to go on without him.  Soon after, while Pete and Murph are asking directions in a small town, a child affixes the "duck's" anchor to a police motorcycle, and Murph is arrested.

Pete travels on until he runs out of gas, and is thrilled to spot Francis, the Navy's new mascot, on the street.  Together, they trick the gas station attendant into filling the tank, and reach the beach only moments ahead of the supply ship, earning commendations from Hutch.  Days later, after Francis and Pete bid goodbye to Slicker and Nancy, they board the train to the Army base.  Once inside, however, Pete is forced to flee from MPs, who still insist that he is an AWOL Slicker, and spends the trip in the barn car with his best friend.

Notes
The working title of this film was The Navy Gets Francis.   A February 1955 HR news item adds Ed Reamers to the cast, but his appearance in the final film has not been confirmed.  Francis in the Navy marked the feature film debut of Clint Eastwood.