As the overture ends, the curtain opening reveals a stage, empty except for a single ghost light. Ladahlord, a strange man, enters and invites the audience to come with him and watch a bizarre, true story unfold. He foretells the adventure they are about to witness ("Right before Your Eyes"). 

The scene transitions to the Painswick Orphanage in London, England, where young James goes to bed, placing a scarf and a pair of glasses under his pillow. These are the last pieces he has of his parents, who were tragically killed by rhinoceros that escaped from the London Zoo. As he sleeps, James relives the tragedy in his dreams. He wakes and holds the scarf and glasses tight. A ladybug and a grasshopper enter (both puppets); James calls to them, promising he will not hurt them. James urges them to leave as this is no place for them; he, on the other hand, has no choice but to stay – he has nowhere else to go. He wishes he could fly off with the ladybug and grasshopper to somewhere warm and welcoming, where he belongs ("On Your Way Home").

The Matron Nurse enters and tells James he's leaving the orphanage. It turns out he has two aunts who are living in Dover – where James is originally from – and willing to take him in. The Matron Nurse tells James he must do whatever his aunties tell him to do, as he cannot come back to the orphanage.

In Dover, we find James' aunties, Spiker and Sponge, on the boardwalk, picking pockets. They extol the virtues of their chosen, criminal profession. They get away with their activities by making charitable donations to the police. A passing Bobby-Cop gives them a telegram that explains about James coming to live with them. At first, they are not sure what do with a child, but then they realize that they can make James their slave. They revel in their latest acquisition.

Spiker and Sponge pick James up at the train station. They assure the Matron Nurse that they will take good care of him, but as soon as she is gone, they show him their true colors. They take him home, which happens to be a decrepit cottage with an overgrown garden... and James will be living in the cellar. Spiker and Sponge then take James' last vestiges of his parents, the scarf and glasses, but James grabs them back. His aunts tell him the only reason they have taken him in is so that he can be their slave; they command him to cut down and old peach tree in the yard. Just then, a spider appears. Spiker kills it and Sponge eats it. James sees the seashore and his old friends from a distance and asks if they can go to the beach. Spiker and Sponge think that is a lovely idea... but they go to the seashore without James! Ladahlord reminds the audience that a magic spell is coming ("Right Before Your Eyes – Reprise 2").

James is about to cut down the peach tree – despite feeling sorry for doing so – when an earthworm and a centipede (also puppets) appear. The centipede chases the earthworm, but James is able to intervenes as the centipede is frightened of him. As James chases the centipede off, he crashes into Ladahlord. Ladahlord gives James a magic book with recipes for potions in it. He promises that, if James picks a spell from the book and devours the potion, fabulous and unbelievable things will happen ("Shake it Up").

James chooses slithering crocodile tongues as his spell. The Ladahlord helps him with the spell and then tells him he must mix the crocodile tongues with water and drink them up, but he warns that whoever meets the crocodile tongues first will get their magic. James runs to the well to get the water, but he trips and spills the contents of the bag. The crocodile tongues chase after a grasshopper, a spider, a ladybug and a centipede.

Spiker and Sponge return to find James in the garden. To their surprise, they notice the old peach tree is growing a piece of fruit, something that has not happened for years. The peach grows bigger and bigger. Sponge wants to eat it, but Spiker won't let her because she knows that people will pay money to see such a phenomenon. Soon, reporters, Hollywood agents and members of the garden guild all show up to see the magic peach. Spiker and Sponge see that they are going to be gazillionaires – all for doing nothing! ("There's Money on That Tree"). Spiker and Sponge sign a variety of contracts, getting sizeable cash advances, for future use of the peach.

James asks if they can use all of the money to move to the seashore or take a trip. Spiker and Sponge make it clear they don't intend to include James in their wealth; James points out that he made the peach grow. His aunts call him a liar and steal his last relics of his parents – the glasses and scarf – and destroy them. Then they punish him further, telling him he must sleep outside. They warn him that he cannot run away because he has nowhere else to go. James realizes that he is stuck, and the time has come for him to make a decision. He notices a door in the peach. Leaving behind his past and present behind, he enters the peach.

Inside the peach, James encounters the insects that ate the crocodile tongues. They are now fully grown, human sized creatures that can talk. Though Centipede is wary of humans – including James – Spider, Ladybug, Grasshopper and Earthworm are more accepting. Suddenly, the peach lurches forward and its stem snaps from the tree, rolling away and running over Spiker and Sponge. It goes across fields, through the village and past a famous chocolate factory ("Right Before Your Eyes – Reprise 3").

James emerges from the top of the peach and realizes that they are floating on the ocean. Though it's not clear where they are heading – Ladybug assumes France – Grasshopper encourages everyone to enjoy the adventure ("Floatin' Along"). Centipede and Earthworm are less certain; they worry that the peach is not seaworthy and that they have no food and water. Ladybug uses an extra pair of her bloomers to create a sail for the peach, and the group is on its way.

Back in Spiker and Sponge's garden, James' aunts recover from having been run over by the peach. They realize that, without the peach, they cannot make good on the contracts they signed and will be in big trouble because they already took the advance money. They hear police sirens and helicopters overhead and they know they better take the money and run ("A Getaway for Spiker and Sponge").

On the peach, James has another bad dream. He and the insects begin telling stories about Spiker and Sponge, and James finds out just how dastardly they really are. Not only did they kill and eat Spider's fiance, they killed Centipede's whole family. Centipede's family were the best shoemakers in the land... until Spiker and Sponge fumigated them. James concludes that Spiker and Sponge were truly terrible, but Centipede disagrees – all humans are like that... including James! Ladybug asks James about his parents; he tells his new friends that his parents are gone. Ladybug disagrees; James' parents are always with him ("Everywhere That You Are").

Ladahlord enters, disguised as a ship's porter ("Right Before Your Eyes – Reprise 4"). He serves drinks to Spiker and Sponge, who are aboard a cruise ship, traveling first class to New York City. Spiker and Sponge have just enough money to get to New York and set up their old routine picking pockets on the boardwalk at Coney Island. They lament having lost the peach when they were so close to having a fortune but, despite having lost nearly everything, they still have each other ("I Got You").

Suddenly, from the deck of the ship, Spiker and Sponge spot the peach floating in the ocean and they insist that the ship "follow that peach!" On the peach, Centipede is feeling a bit seasick. He throws up off the side of the peach, and his vomit attracts a hoard of sharks. The sharks begin eating the peach, and James and the insect crew are in real danger. The vomit has also attracted a pack of seagulls overhead. James has another great idea: using Spider's web as rope, they will attach themselves to the seagulls and fly away. There is just one problem – how will they get the seagulls to fly close enough to them so that they can attach the rope? James has another idea. He convinces the reluctant Earthworm to act as bait, promising he will not get hurt. Earthworm is not pleased with his job, but he calls to the seagulls. As James' plan begins to work, Earthworm becomes more confident in his role ("Plump and Juicy"). Soon, the peach is flying ("Right Before Your Eyes – Reprise 5").

Earthworm is thrilled with the results of their latest escapade, but Centipede is still convinced that James will turn on them. As he climbs to the top of the peach and rails against James, he suddenly slips and falls into the water. James goes in to rescue him, and the other bugs wait impatiently to see if they will ever see either of them again. At last, James and Centipede reappear. Centipede no longer knows what to think of James; how can he think all humans are the same when this human risked his life to save him?

At that moment, they see the top of the Empire State Building. They realize they've made it to New York City! At first, they think they are safe, but then they hear sirens and realize that Spiker and Sponge are on the ground with the police, trying to bring the peach down. An airplane approaching JFK airport flies through the silk threads attaching the peach to the seagulls, and the peach falls from the sky, landing on the spire of the Empire State Building, where it gets stuck ("Right Before Your Eyes – Reprise 6").

Spiker and Sponge run to James. Outwardly, they pretend to be happy to see him and relieved he is okay, but secretly they tell him how they will make him their slave again... after they fumigate the bugs, of course. James stands up to them, telling them they will not hurt his family. At that moment, there is an odd rumbling and the peach falls to the ground, crushing Spiker and Sponge. James asks if it is wrong that he does not feel sad. The insects reassure him that it is okay for him to feel relieved. Centipede says goodbye and is leaving when James stops him. James tells him that he should stay here with them, rather than leaving and being on his own ("On Your Way Home – Reprise"). After all, together they are a family. Though they are a peculiar family, they go on to do incredible things. Centipede becomes a shoe designer; Spider designs bridges with her web and Earthworm forms an activist organization – BAIT: Bugs Against Insensitive Terminology. Ladybug and Grasshopper marry and have kids of their own, but they always think of James as their firstborn son. James goes from being the loneliest boy to having a giant, loving family – all living together in the peach pit ("Welcome Home"). The cast reminds the audience that this was a true story, and it happened right in front of them ("Right Before Your Eyes – Finale").