Molly tries to say it's "time for bubble guppies" but Gil interupts her to introduce each bubble guppy to the audience. Like Little red riding hood, goldilocks, and so on until Nonny tells everyone, "It's time for Bubble Guppies!"
The little fish are on their way to the school and run into Bubble Puppy, who swims to a certain area in the class to sit with all of the guppies. They greet Mr. Grouper and they notice his book and ask him about it. He explains what a Fairytale is and shows them the book while discussing the characters. He then tries to get them to think up some characters, like the wolf from little red riding hood, the three bears, the beanstalk from jack and the bean stalk, and the witch! Then Molly and Gil sings Once Upon a Time.
Deema and the other guppies ask Mr. Grouper to read them the stories inside the book but they all want to hear all sorts of different stories. So Mr. Grouper decides he will tell them a story they have never heard before.
Molly and Gil went up the hill to fetch a pail of water, Molly warns Bubble Puppy not to go into the enchanted forest because he could get lost. Lurking nearby in the shadows was a very mean witch with an evil plan. She then asks her magic mirror who the most evil person in the forest is and she explains her plans of testing a new potion on Bubble Puppy. Nonny points out he is only a puppy but she doesn't care and she blows her magic bubble on the puppy. Bubble Puppy attacks it and he transforms into a frog. She then swims away on her magic broom while discussing her very evil plans involving her mean green bubble potion.
Gil and Molly search for Bubble Puppy but can't find him anywhere until they see a strange frog. They ask the frog if he has seen their puppy and Gil points out the frog is wearing the same collar as Bubble Puppy. They then realize it is Bubble Puppy and Molly asks who could have done this to the poor puppy, then they are informed it was a witch. But Gil doesn't know how they could find the witch until Molly points out her castle is on the whole other side of the enchanted forest.
Meanwhile, in her home the witch is going to make more of her evil potion and again asks nonny who the most evil person is. A few crab assistance come in and she tosses her potion to them and tells them to make her a lot more, enough to fill a truck! She then asks Nonny why he seems so sad and he explains it was because he feels bad for the puppy and after she leaves, he goes to help Gil and Molly. He explains what happened, then warns Molly and Gil they shouldn't come to the castle, instead he will tell them a magic potion to change bubble puppy back. They will need cookies, porridge, and a golden egg. He then adds that they can all be found in the enchanted forest and he takes his leave.
Molly and Gil have no clue where they can find the cookies and they hear someone approaching. It's Oona, as little red riding hood. Oona tells them she likes their cute frog, then when they explain what happened she informs them that her grandmother can probably help them out, so they should follow her. She then tells them they need to skip and soon they head over to find a strange person in Grandma's bed. Oona and the other guppies do not believe this is her grandma though and Oona and the little fish point out how strange she looks. Such as her big eyes, big nose, and big teeth she is. But surprisingly this wolf isn't evil or angry at all! He's very friendly!
Just then Grandma comes into the room with some freshly made cookies. She asks them why they need a magic potion and Molly tells them what happened to Bubble Puppy. And so, Oona decides she is going to come with Molly and Gil to help transform the puppy back to normal, so they can put the food items into her basket.
So leaving Grandma's house, they now need to get porridge. They look into the water pail after Oona asks what porridge is. After he explains and takes his leave, adding that it can't be too hot or too cold, they here someone nearby again and run into Deema, as Goldilocks, singing a little jazz number!
She informs them of how much bears love porridge, so they should just stop by their place to pick some up. She greets the bears family and Molly explains that the witch turns Bubble Puppy into a frog and ask for some porridge. But it has to be just right, it can't be too hot or too cold. Deema shows the little fish and audience the porridge to see which is right. The first bowl is too hot, then the first bowl is too cold, but the final bowl is just right!
They put the porridge away as papa bear warns them to be careful, since the witch is very mean. Deema tells them not to worry though, since she will be going with them and the four continue along their way. They show Nonny that they got the porridge and now they just need to get the golden egg. Nonny warns them to hurry though since the witch plans to do something very cruel and mean....
Meanwhile at the witch's castle, she asks them how it is going and she asks her magic mirror what he may think of all the magic potion she's been having made. Nonny asks what she plans to do with it and she informs him that she is going to be transforming every single person into the entire world into a frog!
The witch takes a momentary stop to explain her evil plan exactly to her assistants. She'll put all of the potion into a rocket, then launch it into space where plenty of green bubbles will form and turn everyone in the world into a frog!
Back with the guppies, Oona asks how they could possibly find a golden egg and Nonny makes another appearance to warn them they need more then just 1 egg, they need 12 eggs! While trying to figure out where they could get some gold eggs, someone else appears. He introduces himself as Jack in the Beanstalk (Goby), and feels badly for them, but all he has are some magic beans, he doesn't have any gold eggs for them. Within a few seconds, a giant beanstalk appears!
The guppies climb up the beanstalk to a castle sitting on top of a whole bunch of clouds. They approach the castle to see if whoever owns it has some golden eggs they can have. Seeing how giant the door is, and how teeny-tiny they are, the guppies simply go under the small crack beneath the door and try to get ahold of someone, but their voices only echo in the lonely room. Oona doesn't think anyone is home when suddenly they feel footsteps and someone coming down the steps. They quickly hide under a newspaper laying on the floor when the giant picks it up. The guppies quickly leave, except for Deema who Oona had to grab and pull away.
They watch the giant who is reading a story about Humpty-Dumpty in the newspaper that day and Molly approaches to ask the giant about the gold eggs. The giant thinks they are mice, despite what Molly tells him. But he calms down but feels sad since his newspaper is all messed up. The begins to cry until the guppies offer to help but the newspaper back together. Goby and the little fish work with the audience to put the story back together.
So now that it is put together, the giant can finish reading the newspaper's story and he asks them how he could repay them for the help. Goby asks if he has any golden eggs, then the giant asks why. They explain what happened and how many they need, then he hands over the dozen eggs and they count to make sure they have enough before thanking him and taking their leave. They then wait for the mirror to respond so that they can tell him they got everything they need. Nonny then tells them the next part will be very hard and he tells them what to do with them once they get there. They need to dump the ingredients into the mean green potion to change Bubble Puppy back to normal.
The guppies then try to locate the castle and they head right on over!
Meanwhile, the witch and all of her assistants have finished putting all of the mean green potion together. The witch tests it out on one random crab assistant as the guppies watch curiously. They see how much potion she has made as Molly points out they need to hurry up and carefully get to the potion. After the witch leaves the guppies quickly sneak by all of the assistants and to the potion area. They hand the ingredients to Molly and Gil, who then carefully make their way over to the potion itself and open the hatch on top of the container.
After they put in the porridge and cookies, they quickly add the gold eggs except for just one of them before an alarm goes off. Molly and Gil worry about the final gold egg they have as the potion is drove off to the launch pad way further down the pathway. Nonny informs them of the witch's plan before being shut off again. The guppies need to hurry up and reach the potion before its blasted off into outer space!
At the sight of the launching area, they watch as the potion fills the rocket. They happen to see a small bridge and try to figure out how they can get into that area to put the final egg into the rocket bottle. The launch sequence is activated before they can reach it when Goby suddenly gets an idea. He takes a magic bean he didn't plant previously and hurriedly digs it into the ground and asks the other guppies to climb it. They can get to the top of it and put the egg inside the potion before it takes off. The witch is excitedly waiting when she happens to see something very tall and green by the launch pad. She asks them about it and tells them to stop countdown. The assistants warn her they cant and she tries to stop it herself.
Molly and Gil get to the hatch but couldn't open it in time and are launched into the sky. The witch demands the mirror to stop them but Nonny refuses. The witch calls for her broom and she goes to stop them herself while the remaining Guppies watch from a distance. Molly and Gil work together to open the hatch as the potion flies into space. With enough yanking they go spinning and drop the egg, which the witch catches!
The witch curiously asks about it, then asks what they were doing. It's then the potion's top part begins to open. She informs them they are too late and without it, nothing can stop the potion. That is, until Bubble puppy uses his froggy tongue to grab hold of it and and he hopes around trying to get it into the mix while avoiding the witch. Gil catches Bubble Froggy and they drop the egg into the potion and watch as it turns a bright sparkly pink color. The bubble wand slowly drifts out of the space rocket bottle and all of the pink bubbles are released onto the world. Gil and Molly watch as the witch is sent flying in an opposite direction.
Millions of pink bubbles begin to appear all over the world, spreading color and beauty throughout it. Nonny is even freed from being just a mirror!
Oona points out something floating down to the ground and inside is Molly, Gil, and Bubble...froggy? Nonny approaches and tells them to hurry up and change the puppy back to normal. Gil holds the little frog up and after a bubble covers him, it changes him back to normal. They thank Nonny for the help, then begin to worry as they see the witch approach. Gil challenges the witch however, saying there isn't any more mean green bubble potion. The witch shows that she still has the original potion however and threatens to use it on them, but Bubble Puppy manages to change the outcome by blowing the bubble on the witch herself, changing her into a frog!
They ask her how she feels about it and the witch actually seems happier as a frog. She thanks them and then hops into the water nearby while all the guppies cheer and laugh. Mr. Grouper ends the story and closes his book as the special comes to an end...
After Mr. Grouper says the title of the movie, the camera moves past a tree and we can see a shadow of the camera.
During the opening of the movie in the classroom, some of the guppies disappear on the stairs.
When Bubble Puppy is playing, he isn't wearing his collar, and when the Witch turns him into a frog, his collar appears from nowhere.