A strange and fantastic red-and-white-striped top hat appears on an empty stage, full of possibilities. A Boy enters and is drawn toward the magical hat. The Cat in the Hat suddenly materializes! "You've got quite a mind for your age," quips the Cat as he/she begins singing about the power of imagination ("Oh the Thinks You Can Think"). Throughout the song, famous characters are introduced who will figure in the musical: Horton the Elephant, Gertrude McFuzz (the bird with the one feather tail), the Whos of Whoville (including the Mayor and his Wife), Mayzie La Bird, the Sour Kangaroo and the Citizens of the Jungle of Nool. The Boy and the Cat use their imaginations to transport everyone to the Jungle of Nool as the adventures begin.

Horton is splashing in a pool when he hears a distant cry for help. ("Horton Hears a Who"). He follows the sound to a tiny speck of dust floating through the air and realizes that there are people living here, so small they can't be seen – the tiny citizens of Whoville. Horton vows to help them and places Whoville safely onto a soft clover just as Sour Kangaroo and her baby arrive. The Sour Kangaroo thinks Horton is crazy for talking to a speck of dust and she and the rest of the Jungle Citizens mock him for his delusions. ("Biggest Blame Fool"). The rascally Wickersham Brothers – a cool group of bad-boy monkeys – join in the fun of teasing Horton. The Cat in the Hat weaves through the number, taking on the persona of a talk show host who interviews everyone in the jungle, including Mayzie La Bird and her backup group of Bird Girls. The one person who stands up for Horton is his neighbor, Gertrude McFuzz, who is not noticed by anyone, least of all Horton.

As Horton is left alone with his inhabited clover, the Cat, who is always around, throws the Boy into the story – he becomes Jojo, son to the Mr. Mayor and Mrs. Mayor of Whoville. Horton discovers much more about the Whos and their tiny town of Whoville ("Here on Who"). Mr. and Mrs. Mayor are both very unhappy with Jojo because his "Thinks" have gotten him into trouble at school. ("How to Raise a Child") They tell him to take his bath and go to bed, but the Cat has another idea, ("Oh, the Thinks You Can Think – Reprise") and Jojo's imagination gets the better of him. His bathtub becomes McEligott's Pool, full of fantastical fish ("It's Possible")! The fun is interrupted when Mr. and Mrs. Mayor rush in because Jojo has flooded the house with bathwater.

Horton sits alone, guarding the clover ("Alone in the Universe"). Horton and Jojo hear each other and become friends when they realize their imaginations are so much alike – "one true friend in the universe who believes in me."

In another part of the jungle, Gertrude has just written her 427th love song about Horton ("The One Feather Tail of Miss Gertrude McFuzz"). She believes Horton doesn't notice her because of her small and uninteresting tail. Mayzie appears with her Bird Girls, and offers advice ("Amayzing Mayzie"), which leads Gertrude to Doctor Dake (played by the Cat in the Hat) and his pills for "amayzing" feathers. After taking too many pills, Gertrude is very happy as her tail begins to grow ("Amayzing Gertrude").

The Wickersham Brothers are up to no good ("Monkey Around"). They decide to steal the clover with Whoville on it. They ambush Horton, grab the clover, and "Chasing the Whos" begins as the monkeys tease Horton and he huffs and puffs after them all over the Jungle of Nool. The Cat in the Hat plays a helicopter newscaster tracking the chase. The Wickershams eventually hand off the clover to "a black-bottomed eagle named Vlad Vladikoff," who flies off with the clover and drops it directly onto an enormous field of clover.

Horton begins looking for the Whos, clover by clover by clover. Gertrude has followed the chase and arrives with her new, incredibly long and unwieldy tail, determined to tell Horton how she truly feels ("Notice Me, Horton"). But Horton is oblivious, looking for the Whos. Gertrude leaves, rejected and sad.

Mayzie La Bird calls to Horton from her nest in a tree. She's bored to death, ("How Lucky You Are – Reprise") and convinces Horton to sit on the nest for her while she takes a brief vacation ("Horton Sits on the Egg").

Seasons pass, and Horton is still stuck, sitting on the egg. The Whos are still lost in the clover, and Gertrude still cannot get Horton to notice her and her new long tail. Hunters suddenly arrive, capture Horton and the egg and take him away. ("Egg, Nest and Tree"). After a long, arduous trip, Horton arrives in New York, where he is auctioned off to the circus. The "Seusseby's auctioneer" is played by the Cat, and allows the audience to bid on Horton.

The traveling circus lands in Palm Beach, where we find Mayzie under a palm tree, bemoaning the monotony of vacationing ("Mayzie in Palm Beach"). She decides that she needs a change of scenery and heads to the circus, where she runs into Horton. He begs her to take back her egg., but Mayzie decides Horton would be a better parent for her egg than she could ever be ("Amayzing Horton"), so she gives him the egg for good and leaves before he can say no. Horton accepts the responsibility of caring for the egg ("Alone in the Universe – Reprise"), even though he worries about Jojo and the Whos. He sings the egg a lullaby ("Solla Sollew") that is echoed by Jojo and Mr. and Mrs. Mayor.

Gertrude finds Horton asleep in his cage. She has managed to get rid of her unwieldy tail and has journeyed great distances and through much peril ("All for You") to find and rescue him. At the end of her number, she mentions one more thing – she also has found the Whos' clover! Horton finally notices that Gertrude is amazing.

But, just as Horton finds the Whos again, the Sour Kangaroo and the Wickersham Brothers show up and make a citizen's arrest. They take Horton back to the Jungle of Nool, where he is put on trial "for talking to a speck and sitting on an egg." The trial begins ("The People versus Horton the Elephant") and Judge Yertle the Turtle sentences Horton to the Nool Asylum for the Criminally Insane. The speck of dust is ordered to be boiled in oil. Horton trumpets his protest and tells the Whos they must yell to be heard. They have to prove they exist, and there's no time to lose!

The Whos scream and make as much noise as they can, but still only Horton can hear them. Suddenly, Jojo comes up with a Think: a new word to shout that will be heard by everyone--YOPP! At the last minute, all the animals of Nool hear Jojo's cry and Whoville is saved. Just then, the egg begins to crack – all gather around as the new baby emerges – and they are astonished to see that it's... an Elephant Bird! Horton looks to Gertrude for help, realizing that she is his "one true friend in the universe," and she agrees: "You teach him earth and I will teach him sky."

As the show ends and all are united, the Cat hints that many more adventures are likely to occur "if you open your mind, oh, the thinks you will find" ("Oh, the Thinks You Can Think – Reprise"). All the characters vanish, leaving The Boy alone onstage with the red-and-white-striped hat, the embodiment of his imagination. As he puts it on, it falls over his eyes, putting the stage into BLACKOUT!