Episode 1: Surprise is playing about and scares the other Ponies while out walking. Baby Cuddles jumps across the other ponies in fright and lands on Spike. Gusty tells Surprise to knock it off as they’re on there way to Flutter Valley and are already late for the celebration. Gusty blames Cupcake for their lateness as she had to bake a cake. The witches Hydia, Reeka and Draggle are watching them through a pool of water. They plan to ruin the flutter ponies’ celebration. Hydia sends her daughters out to stop the group making it to Flutter Valley. They use a spell on some Daisies, turning them into ropes to lassoes the ponies. They catch them ruining Cupcakes cake. The flutter Ponies had got worried when the group hadn’t shown and went out looking for them. They spot them with the witches and switch to utterflutter, a faster fluttering of there wings. Thanks to the pollen and the Flutter Ponies the group of Ponies get away while the witches worry about what Hydia will do to them. The witches decide to go to Flutter Valley too. At Flutter Valley Rosedust Queen of the Flutter Ponies, declares the day Sun Tuesday under a golden Sun Stone while the witches try to find another spell. The Bushwoolies hand Rosedust cakes she thanks them then Cupcake offers her Chocolate cake looking a bit ruin. Suddenly the earth shakes; the witches had use a land slide spell and the ponies run for covers. The Sun Stone looks like it’s about to fall.

Episode 2: The two witches think they have them when mud starts flying back up at them. It turns out Draggle had made a land pie as well, they run off and the ponies cheer. The Flutter Ponies Honeysuckle and Morning Glory argue whether to get revenge or not on the witches but Rosedust calms them down and the ponies tell the Flutter ponies they have to leave for home. The two witches get back to the volcano to a telling off from Hydia and she just can’t understand why they’re not evil enough. Hydia calls her family to her from out of paintings and they give her an idea to steal the Sun Stone and take over Flutter Valley. The girls go to find Bumble A big bumble bee, and her bees to help capture the Flutter Ponies and Sun Stone. Finding her the witches introduce them selves and convince Bumble she wants the Sun Stone off the Flutter Ponies who she hates and to help them. Spike watches for more witches when Surprise flies in warning the other ponies of creatures ahead. They find Furbobs friends of the Bushwoolies and they run over to say hello and introduce themselves. Where the Bushwoolies always agree the Furbobs never do. The Furbobs explain the Stonebacks are chasing them from everywhere they live. Just then the Stonebacks start eating the bridge they look like armoured armadillo with crocodile mouths.

Episode 3: The ponies are on the bridge calling for help, the bridge breaks and Fizzy makes a bubble with her horn that the Bushwoolies and Furbobs fall onto. Surprise saves Spike and Baby Cuddles dropping them face first in some mud. The others fall in some near by water. The Furbobs can’t remember why the StoneBacks hate them and Baby Cuddles has hurts her leg. They decide to go to Furbobia as it was closer then Paradise Estate. The daughter witches try a spell of a rainbow with Bumble and steal the Sun Stone, they succeed and the flutter ponies chase the bees into Bumbleland. Bumble asks Sting her guard to prepare the honeycomb. The Flutter Ponies’ spot the stone on the floor, as they swoop in to get it Sting drops the Honeycomb on them trapping them inside. Bumble gets Sting to place the stone to warm the land while the witches enjoy their new home making it dark and dirty. Still unable to find Furbobia the ponies carrying Baby Cuddles on a raft rest. They tell Baby Cuddles not to worry while wishful the Bushwoolie wishes for some apples that fall straight off the tree in front of them. Surprise pushes them on reminding them the sun will be setting soon and they run into more StoneBacks. Bumbles land is flourishing and she starts eating all the flowers while the Flutter Ponies argue again. Honeysuckle suggests a plan to blown down the wall and escape. They shift to utterflutter and Bumble covers them with honey to stop them suggesting they’ll be her slaves.

Episode 4: Bumble is still tipping honey in but Sting reminds her she doesn’t want to drown them. Morning Glory hadn’t got hit as much as the rest and escape out of a window in the honeycomb, she’s chased but makes it to freedom. Surprise is trying to distract the Stonebacks but it wasn’t working. The other ponies too try but nothing works till Buttons drops a lot of apples on them and they run for it finding the Furbobs home. They tell the furbobs about Baby Cuddles leg and the Furbobs call out “prepare the steamer”. Meanwhile Morning Glory is getting tired the honey on her wings is slowing her down and making her heavy. The bees find her and she has to fly again but they capture her and take her back to Bumbleland. Bumble is feeling rather full after too much nectar when the bees drop Morning Glory in front of her. She gets Sting to put Morning Glory into a cage just before she falls to sleep. Baby Cuddles is scared about what’s going to happen to her. The Bushwoolies reassure the ponies that the Furbobs won’t hurt her. During the song Baby cuddles is in a box and the Furbobs make her float on multi coloured steam when she lands she’s all better. The ponies decide to help with the Stoneback as they’ve helped them; they decide to go back to Flutter Valley to get the Flutter Ponies. The daughter witches are having second thoughts about leaving the volcano of doom their home but Hydia still insists on it.

Episode 5: Bumbleland is getting so hot a bee Pointer, burns his finger on a flower. He dips it in the only tiny ice patch left that had once covered the land. He wakes up Bumble and tells her about the Sun stone she ignores him and goes back to sleep. The Flutter Ponies notice it’s getting hotter, Morning Gory tries to change Sting’s mind to let her go and return the Sun Stone. She learns he can’t fly so she teaches him. She almost gets away but Sting remembers his job and locks her back up. The ponies make it back to Flutter Valley and find its awful now. They’re greeted by Hydia and her daughters. They brag about having Flutter Valley but the ponies fight them. The ponies then have to run from Ahgg but he drops a web on them trapping them. Back in Bumbleland the Sun Stone has coursed a fire, the whole kingdom burns while bees drop water all over it. The bees abandoned Bumbleland and Morning Glory points it out to Sting Bumbleland is burning.

Episode 6: Back with the Flutter Ponies the fire still rages but it’s melting the honeycomb. The Flutter Ponies are hoping it’ll melt enough for them to escape. Morning Glory is finally freed by Sting when he realises Bumble has left him and he knock the Sun Stone to the ground burning a hole in the floor. Morning Glory then explains to him Flutter Valley is finished without it. Bumble returns and tries to get Sting to lock Morning Glory back up but he refuse and claims the Flutter Ponies as his friends. So Bumble orders Pointer to take Sting prisoner too. Sting and Pointer fight in the air with Sting the winner before they fly away and the Flutter Ponies escape from the honeycomb on hoof only to be stopped by the bees. Hydia and co are still waiting for Flutter Valley to turn dark. The other ponies have been strung up in a tree, in a web net. Fizzy comes up with an idea and uses her bubble power on the Furbob while the ponies ask Ahgg to let him out so Ahgg can play with the Furbob. Ahgg does and the bubble pops letting the Furbob run off for help to Hydia’s dismay. Sting and Morning Glory work on how to save the Flutter Ponies and Sun Stone when a rainbow appears. Morning Glory explains Megan lives on the other side of the rainbow and is hoping she’ll help them so they fly along it. They make it to her house but can’t find her instead they find a bull.

Episode 7: The bull is still chasing after Sting and Morning Glory, Sting knocks himself out trying to escape. So Morning Glory tries to distract the bull while Megan rides in luckily in time to help. Megan fetches the red blanket off of her horse and flags the bull back into its stall. Morning Glory and Sting explain what’s going on and they set off for Ponyland. The witches try to turn the little ponies purple instead turn them selves purple so they have to go all the way home to wash it off. The furbob realises he doesn’t know where to go for help just when Morning Glory and co drop in to ask about the other ponies. Bumble has had to go back to the old ways of finding flowers. Having run out, she orders the Flutter Ponies to her and asks them to get the Sun Stone back. She makes them dig the hole bigger while Pointer tries a crane to lift it out. Honeysuckle makes an excuse she wants a drink before spitting it up in Pointers face and taking over the crane. She lifts up Bumble and puts her over the hole. Pointer tries to help Bumble by cutting the rope and dropping her chair into the hole while Bumble jumps off. The bees then go on the attack again after the Flutter Ponies. Bumble ends up tripping Honeysuckle into the hole.

Episode 8: The Flutter ponies call out to see if Honeysuckle is ok but they hear no reply. Pointer puts the Flutter Ponies back to work while Megan tries to talk to Bumble. She tells Bumble she’s surrounded and twigs twitch all around them. Pointer knocks Megan; Sting goes to fight Pointer again while the Flutter Ponies try to escape again. This time Pointer wins and Bumble traps them all in another cage marching the Flutter Ponies back to work. The other ponies are trying to cheer up Draggle and they try to convince her to let them go. They offer Draggle pony magic before breaking out into song to show her. They trick Draggle into letting them go and tie her up but it isn’t long before the ponies are caught in another “fly” trap by the witches. Morning Glory is getting upset that there’s not much time left, Bumble runs out of flowers and Honeysuckle climbs out of the hole freeing Morning Glory and co. She tells them to get the flutter ponies to go down the hole and Bumble and her bees have a surprise coming. Honeysuckle’s brought the Stonebacks with her who attack Bumble. With the Flutter Ponies free Honeysuckle calls off the Stonebacks and escapes herself, Leaving Furbob at the top of the hole.

Episode 9: Bumble closes in on the Furbob but they pull him into the hole. The Ponies all start to fill in the hole. Bumble tries to go down the hole after them but gets stuck. Megan tries to convince the Furbob that the Stonebacks may want to just be friends with them but he has to check with the others first before he can agree. The Flutter ponies use utterflutter to cool off the Sun Stone and rush off with the stone to Flutter Valley. The Stonebacks dig them out and the Furbob goes with Sting to get the other Furbobs to help drive out the witches. Hydia is making Draggle run around carrying the spell book when she spots the Flutter Ponies. Hydia sends Ahgg to stop them after giving him a potion to stop him being tickled this time like they did in the first movie. Megan does try to tickle Ahgg but nothing happens.

Episode 10: Ahgg still has them trapped; Megan uses the Stonebacks to tunnel under Ahgg. The witches toast to their certain win. The furbobs and Bushwoolies turn up to help dig the tunnel under Ahgg. They make it to the other side and Ahgg falls over into his web. The witches run away as the Flutter Ponies realise the other ponies. They put the stone back just in time when Bumble turns up to steal it again. Sting gives Bumble some home truths and Rosedust offers that Bumble can come back any time to help herself so Bumble thanks them and leaves. The Sun Stone starts to restores the land and Morning Glory and Honeysuckle apologize to each other. Just when everything seemed fine a cloud turns up to block out the sun. It’s the witches trying one last attempt at claming Flutter Valley. The Flutter Ponies blow the cloud away and get the witches by blowing them away too. They then celebrate as the Valley gets back to normal.

Our film opens with the arrival of spring and the ponies planning the Spring Festival, including Baby Lickety Split who is coming up with some creative dance moves. Meanwhile, our witchy villains are  watching them through a potion with disgust. Hydia believes her daughters are not living up to her evil standards, and send them to ruin the ponies festival.

We return to the festival to watch the baby ponies dance, and Baby Lickety Split gets ahead of herself with her dance moves, runing the performace and upsetting Buttons and the other baby ponies who berate her until she runs away in tears. Baby Lickety Split decides to run away though Spike does his best to stop her.

Reeka and Draggle have made it to Dream Valley, and are trying to figure out how to ruin the festival. Draggle uses a spell to shoot water from a water fall to drown out the festival, but are thwarted by seaponies. They wash out to the festival where they are called "cute", and leave, offended.

Baby Lickety Split attempts to fly over a cliff but, since she's an earth pony, plummets down with Spike in tow and gets stuck. The other ponies realize the two are missing and believe she may be with the Bushwoolies. 

Disappointed in her daughters' failure, Hydia decides to use the Smooze, a purple goo that previously destroyed Grundleland. First she needs the proper ingredients, and the witches are sent out once again. Baby Lickety Split and Spike try to get up the cliffside with little luck while the sisters explore the swamp for ingredients. Hydia begins prepping the Smooze recipe by throwing the ingredients into the volcano, creating the Smooze despite missing an ingredient. It flows down the volcano and into Dream Valley.

The other ponies pass right by Baby Lickety Split and Spike, unable to hear their cries over the waterfall. They meet up with the Bushwoolies, who are on their way to the Festival. Both parties are stopped when the Smooze rushes in. Magic Star takes the smoozed Gusty and all but one Bushwooly back to Dream Castle, leaving Shady and her Bushwooly companion to continue the search. The smooze has reached the trench where Baby Lickety Split and Spike are trapped, forcing them to retreat into the cave. Magic Star and the others reach Dream Valley just in time, ushering every creature and pony into Dream Castle.

North Star and Wind Whistler go to find Megan, who is with her siblings. They initially come only for the Rainbow of Light, but all three convince the ponies to let them aid in the fight.

Back at Dream Castle, the ponies are attemping to barricade against the Smooze, but it is too strong. The pegasi arrive with Megan and her siblings, and she unleashes the Rainbow of Light, which is eventually defeated after a battle. The Smooze is revealed to be weakened due to the sisters forgetting to get one specific ingredient. Megan, North Star, and Fizzy leave to seek out The Moochick while the sisters work together to get some Flume to strengthen The Smooze.

Megan and her pony companions reach Mr. Moochik, who reveals he has no more Rainbow for them, and instead sings about the types of homes the ponies can find now that Dream Castle has been smoozed. He creates Paradise Estate for them and informs them that the Flutter Ponies are the only ones who can take care of The Smooze.

Spike and Baby Lickety Split are trying to find a way out of the cave the Smooze trapped them in. They come across The Grundles, who convince them that, though they appear scary, they are quite good. Their kingdom has already been destroyed by The Smooze, and they offer to help the two.

The witches toss their acquired Flume into the Smooze so it can reach it's full potential. Back in Dream Valley, the ponies are excited to explore Paradise Estate. The celebration doesn't last, as the smooze is coming back with a vengeance. Shady continues to struggle to find Lickety Split. We cut back to the volcano where the sisters are told to seek out Ogg, bringing an offering of food.

Shady's distress is cut short when the smooze reaches her. Megan, Danny, Molly, Fizzy, Magic Star, and Wind Whistler seek out Flutter Valley, narrowly escaping threats such as The Smooze, evil trees, and a giant spider. They meet up with Shady and her Bushwooly along the way.

The Grundles, Spike, and Baby Lickety Split also have a run in with the smooze that they escape, though Spike gets a little of the goo on his tail. They land in a flower field near a well, and Baby Lickety Split sings into it. At first they believe the voice inside is an echo, but after it sings back they discover it's actually a Flutter pony, Morning Glory. She offers them help since they rescued her from the well, and they head for Flutter Valley. They reach Flutter Valley and meet Rosedust, who turns them down. Suddenly, Morning Glory arrives with Baby Lickety Split and the others, finally reuniting the groups. They beg Rosedust to assist them as The Smooze begins to reach Paradise Estate.

Hope seems all but lost as the Flutter Ponies and the others arrive, pushing back The Smooze with the gusts of magic from their wings. Dream Castle and Dream Valley  are freed from The Smooze as the witches are chased back to their volcano. The Grundles are offered Dream Castle as thanks for their help in keeping Lickety Split safe. The Flutter Ponies return home, the Rainbow returns to it's locket, and Megan and her siblings head home knowing Dream Valley is safe.

For now...