The show begins with the dawn of a glorious summer's day out in the country. Standing in the sunshine is a small farm, behind which is a lake surrounded with cattails. Drake, a proud father-to-be, introduces us to "A Poultry Tale." His wife, Ida, and the rest of the farmyard residents join in the telling while the Cat hides, eyeing the duck eggs in Ida's nest, which he hopes will make a savory dinner. As the assorted barnyard animals rush offstage, Ida remains to tend to her nest of four average-sized eggs and one curious-looking, large brown egg. Ida is bossy and irritable after tending the eggs for such a long time and she complains to Drake about her cramped quarters and his unwillingness to shoulder some of the burden. After Drake makes a hasty exit, Ida sings affectionately about "The Joy of Motherhoood" with a neighboring moorhen, Maureen. They exchange observations on the anguish and happiness of bearing children just as the eggs start cracking. Four perfectly respectable ducklings emerge from the four perfectly respectable, average-sized eggs. After Maureen coos over the newly hatched ducklings, she goes off in search of Drake to tell him the good news. While the wide-eyed newborns yearn to explore their new world, their mother strictly lays down a few "nest rules" for her youngsters. Drake returns to meet his new children just as Ida realizes that the large egg has yet to hatch. Though Drake tries to persuade her to leave the big egg and join him and their ducklings for a swim, Ida insists upon staying with her unusual, unhatched egg. Drake joyously races the children down to the lake for their first swim while Ida resumes her position on the nest. Ida contemplates the last remaining egg and broods about why this one is so "Different." Suddenly there is a chipping sound, followed by a cracking sound. Ugly, a large, ungainly bird waddles out of his shell with a loud "HONK!"

Ugly cannot quack like the others. He is much larger than the others. Ida worries that her new hatchling is indeed a turkey — as Drake suggested — but Ugly allays her fears when he doesn't react to the word "Butterball" and is eager for a swim. Though at first taken aback by her unusual child, Ida hugs her duckling and all is well between mother and son. They make their way to the pond for his first swimming lesson. Ida instructs Ugly on the various joys and dangers of swimming in "Hold Your Head up High." Ida soon realizes that Ugly is an amazing swimmer and he is exhilarated and joyous until he meets Drake and the ducklings on the shore. They humiliate their awkward sibling with "Look at Him." Ida tries desperately to defend Ugly as the ducklings, along with the neighboring animals (and even his father, Drake), taunt and tease him unmercifully.

Grace, a duck so lovely that she is honored with a red band, meets Ida's new offspring and congratulates her — but only on the perfectly respectable ducklings. Ugly suffers further humiliation from the members of the barnyard when they gather for a taste of French bread thrown into the pond, but he is crowded out and unable to share in the feast. Alone, hungry and miserable, Ugly laments his fate of being "Different," but, at the end of the song, the devious Cat sidles up to him, commiserates and persuades Ugly to join him for "lunch" in his den. When Ida realizes that Ugly is missing, she organizes a search. Cat and Ugly arrive in the conniving feline's kitchen. Cat prepares his delectable repast a' la Julia Child's cooking program. He encourages Ugly to "Play with Your Food" as the innocent but hungry duckling joins in — never realizing the Cat's dubious intentions. By chance, a baseball whizzes into the Cat's lair and strikes him on the head. When the child who hit the ball decides to retrieve it, Ugly becomes frightened and decides to go back to the duck yard, leaving the unconscious Cat behind. However, as Ugly tries to retrace his steps, he realizes that he is lost. Meanwhile, back at the barnyard, the neighbors are certain that a culinary death at the paws of the wicked Cat befell poor Ugly, but Ida refuses to believe it. Suddenly, the fate of the missing fowl becomes a media event when Drake invites Jay Bird of "America's Most Feathered" to do a feature story about the missing duckling. In her television interview, Ida sings a heartbreaking "Every Tear a Mother Cries." She then sets out on a journey in search of her not-so-little, but very lost ugly duckling.

On the marshlands, Ugly has sought shelter in a ditch. There, he encounters Greylag (a stern, admiral-sort-of gander) and his wife, Dot, who are looking for their wayward flock of geese. Ugly asks the flighty pair for directions back to the farm, and the geese offer to help Ugly find his home. They advise Ugly that the Cat is not his friend and, since it is hunting season, they warn him to stay out of sight. The military-minded Greylag assembles his squadron of geese to join him on "The Wild Goose Chase," but who should pop up on the scene promising to take Ugly back to his disconsolate Mom? The Cat. Greylag, however, won't buy it and has taken personal charge of the duckling's safety. The Cat warns them not to fly while the hunters are about, and he magnanimously offers to spy on the hunters and to advise Greylag "when they are putting away their guns." Greylag, although wary, agrees. When the Cat assures the geese that it is safe to fly, Greylag insists that the Cat join them with a parachute. Cat, Greylag and the flock fly off in search of Ugly's mom, leaving Ugly, the poor lost soul, safely behind. But, as soon as the search party is airborne, shots ring out and feathers fly. Ugly now knows that the Cat is deception "purr-sonified" and never to be trusted. He's learned a valuable lesson, but he is still lost.

Meanwhile, back at the duck yard, Drake is burdened with the brunt of the responsibility of minding the brood ("Joy of Motherhood – Reprise"). Ugly, who is still lost, encounters Penny, the most beautiful bird he has ever seen, tangled in a fishing line. A chivalrous Ugly comes to the lovely swan's rescue. When Penny learns that Ugly is lost and alone, she eagerly suggests that he join her flock, fly south for the winter and then they will both search for his family next spring. Obviously attracted to this beautiful swan, Ugly is tempted, but he opts to stay and search for his worried mom. Penny embraces Ugly and takes off with a resounding "honk." Ugly is confused when he hears the familiar cry. He has been touched by the snowy-feathered, beautiful Penny, but he despondently concludes that she will forget him. Before he can get too maudlin, a Bullfrog with a Lily Pad under his arm jumps in front of the heartsick Ugly. The Bullfrog soon realizes that Ugly has a problem with his appearance. No stranger to denigration because of uncommon attributes, the Bullfrog cheers Ugly up and teaches him to love himself with "Warts and All."

Sufficiently cheered up and with a much better attitude, Ugly bids the Bullfrog and his Froglets goodbye. But as soon as the frogs depart, a farmer ensnares Ugly in his net and threatens to turn him into his family's Sunday roast. When the farmer briefly retreats, the Cat appears and offers Ugly a dubious proposition: he'll help Ugly escape the net and the farmer's fate to reunite Ugly for one last farewell with his mother... if Ugly will agree to be the Cat's main course. Desperate to see his mother and realizing that he's a dead duck either way, Ugly agrees to this ill-fated plan.

Throughout Ugly's journey, the seasons have changed. As Cat and Ugly make their way back to the barnyard, they are caught in a late winter "BLIZZARD." They fight desperately to make their way through the snow, but as the storm blows over, Ugly and Cat succumb to the weather and are completely buried beneath a snowdrift. Ida, having searched far and wide, recognizes her offspring's figure in a lump of snow and, realizing that she is too late, approaches her son's icy grave. As she sinks to her knees sobbing, Penny and her swan family have returned. Mother Swan sees Ida and encourages her tears, "for the warmth of a mother's tears can thaw the stoniest frost." As she turns away in frustration, Ida's warm and salty tears melt the snow, revealing her ugly duckling. The ice falls from his feathers, and Ugly emerges as a beautiful swan. "I'm not a duck" he honks, "I'm a swan!" Ida and her handsome Ugly embrace. Penny appears; their love is instantly rekindled. Ida, in her motherly wisdom, recognizes true love when she sees it.

So, despite the heartache of saying goodbye to her son, she sends Ugly off with his lovely Penny to learn the ways of the Swans. She follows the swans flying off and tearfully misses her son ("Different – Reprise"). Suddenly Ida hears a joyful "Honk!" from behind her. Ugly declares that he could never leave his true mother who raised and loved him unconditionally. Penny and Ugly decide that they will be the first swans to live on the duck pond. Ugly is proud to be different, and he likes his "Honk." Ida beams with pride. But, before they return to the barnyard, there is some unfinished business. Ugly taps the other lump of snow. The ice chips away and a rather batty Cat breaks out singing a befuddled "Melting Moggy." ("Moggy" is a British word for a house cat.) After all the Cat has been through, he has cracked up and is no longer interested in duck or swan dinners.

In the finale, ("Look at Him – Reprise") Ugly, Ida and Penny return to the barnyard with a flourish. The ducklings, the neighbors – and even Drake – now extol the virtues of having such a fine bird in their midst. Grace, previously the prettiest duck on the lake, graciously relinquishes her coveted red band to the handsome Ugly. The whole neighborhood has learned how important it is to "just believe in yourself. Don't be left on the shelf feeling that all hope is dead and gone. And you may find, in your own way, you're a swan."