The Ponies are on their way to Flutter Valley for the "Sun Tuesday" celebration with the Flutter Ponies. Meanwhile, the Witches from the Volcano of Gloom are busy hatching a plan to destroy Flutter Valley and the Ponies.

The witches from the Volcano of Gloom have devised a way to steal the Flutter Ponies' Sunstone. Without the Sunstone, Flutter Valley will wither and die! The witches have enlisted the help of Queen Bumble and the bees from Bumleland, who also hate the Flutter Ponies, to steal the Sunstone and take it to Bumbleland where it will help flowers grow so they have all the nectar they need. The witches in turn will get Flutter Valley, which will be dark and gloomy without the heat of the Sunstone.

The Bumbles steal the Sunstone and take it back to Bumbleland, where it promptly melts the snow and grows hundreds of flowers. The Flutter Ponies are captured and put in a honeycomb prison. After trying to use their wings to blow the prison apart, Queen Bumble orders honey to be thrown into the prison to immobolize their wings. Meanwhile, the other Ponies are trapped on a rope bridge with the Furbobs and the Stonebacks are eating the ropes at both ends of the bridge. The bridge breaks and they all manage to land safely, except Baby Cuddles, who broke her leg. They decide to take her to Furbobia to mend her leg.

Morning Glory manages to escape the Honeycomb Prison, but her wings still have honey on them, and she can't fly fast enough to escape Queen Bumbles' swarm. She is recaptured and guarded by Sting in her own cage on the other side of Bumbleland. Meanwhile, the Ponies finally make it to Furbobia and the Furbobs fix Baby Cuddles' leg. The Ponies decide that to repay the Furbobs for their kindness that they will help them fight the Stonebacks. The Ponies realize that they will need more help and head back to Flutter Valley to ask the Flutter Ponies to help them fight the Stonebacks. The Sunstone starts to overheat Bumbleland, but no one seems to notice...

Bumbleland continues to get hotter and hotter as the Sunstone overheats. By now the flowers and trees are catching fire. Sting and Morning Glory start to bond while he is guarding her, and he lets it slip that he can't fly. Morning Glory offers to teach him, but Sting won't let her out of the cage. The Ponies make it to Flutter Valley, but are ambushed by the witches and their giant pet spider. All of Bumbleland catches fire and Queen Bumble orders for the swarm to put out the fire, but by now it's too late! She and the rest of the swarm evacuate, but they leave the Flutter Ponies behind, trapped in the Honeycomb Prison in the middle of the fire!

Morning Glory and Sting escape Bumbleland to find help.

Morning Glory and Sting convince Megan to come back with them to Ponyland to help save Flutter Valley.

Megan and the others come to free the Flutter Ponies, but end up captured themselves!

Furbob is afraid of the Stonebacks, but Megan convinces him that they are friends, not enemies.

Will the ponies be able to get the Sunstone back in place to save Flutter Valley before the sun sets?

There's a menacing ghost inside Paradise Estate! The ghost turns out to be a shape-shifter named Pluma, who has come to reclaim half of an amulet that is buried underneath Paradise Estate. She's been forced to find the amulet by Squirk, who has kidnapped her grandfather until she can bring the amulet to him. Once Squirk has both halves of the amulet, he will be able to use his powers to flood Ponyland.

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A pair of monkeys called Gizmonks take Danny and Surprise prisoner until Megan turns over the Rainbow of Light to them.

Dream Valley is full of activity as the Little Ponies train for the Pony Olympics. What the ponies don't know is that three Raptorians are flying overhead in search of magical material to repair Princess Porcina's cloak. The Raptorians think their search is over when they discover that the ponies are magical creatures. Meanwhile, Shady confides in Molly that she feels like everyone can do something special except her.

The Bushwoolies spy the Raptorians taking Lickety-Split, Gusty, and Heart Throb to the Black Mountains and rush to Paradise Estate to tell the others. Megan takes Magic Star, Paradise, and North Star to rescue them, letting the Bushwoolies lead the way. None of them notices Shady and Molly secretly following as backup rescuers. While the rescue is taking place, Lickety-Split, Gusty, and Heart Throb learn what will happen to Ponyland once Porcina's cloak is repaired.

The Raptorians discover that the captured ponies' hair grows back instantly once cut off. Not only are Lickety-Split, Gusty, and Heart Throb then forced to stay, but they are also ordered to weave Porcina's new cloak themselves. The search party is reunited with the catpured ponies only after the magic cloak has been finished and delivered to Porcina. The captives inform the others of Porcina's threat to turn Ponyland into glass and the Raptorians' plan to claim it as their new kingsom. Before anything can be done, Porcina has cast a spell through her mirror that turns all of Ponyland and every creature living there into glass.

Shady and Molly reveal themselves to their friends; Shady then devises a plan to make a fake cloak out of shed Bushwoolie hair so that they can exchange it for Porcina's cloak and reverse the spell. Everything goes fine until the switch has to be made: the lights go out, the cloaks get mixed up, and Megan is forced to guess which one is real when the Raptorians arrive. Porcina tries to turn the intruders into glass but cannot bring herself to cast the spell – these beings are more real to her that the poor souls she transformed through her mirror. Her hesitation causes the Raptorians to turn on her and steal her cloak so that they can cast the spell themselves. But it turns out Megan took the right cloak after all. This brings about a tug-of-war that tears the cloak, releases its magic, and turns the Raptorians into glass. Princess Porcina repents her old ways and restores Ponyland and the Little Ponies before moving in with the Bushwoolies as their new hair groomer.

The Ponies find a puppy and decide to keep her and build her a doghouse and name her Dinah. When the new puppy is reunited with her family the following Spring, the Ponies are sad to see her go, but they realize that even though friends come and go they will never leave their hearts.

Baby Heart Throb, Baby Lofty and Baby Half Note want to sing backup for Knight Shade. But to their dismay, he has stolen their shadows, which contain all of their energy and substance. The Ponies soon discover that the evil wizard Arabus is behind Knight Shade's behavior, and now it's up to the Flutter Ponies to save the day.

Baby Heart Throb, Baby Lofty and Baby Half Note want to sing backup for Knight Shade. But to their dismay, he has stolen their shadows, which contain all of their energy and substance. The Ponies soon discover that the evil wizard Arabus is behind Knight Shade's behavior, and now it's up to the Flutter Ponies to save the day.

Megan and Molly take Baby Heart Throb, Baby Lofty and Baby Half Note to a concert featuring their favorite singer, Night Shade and his back up singers, the Shadowets. After the concert is over, Baby Heart Throb and the other baby ponies meet Night Shade and get their shadows stolen, which leaves them feeling sick and very dizzy. They are soon trapped in a cage by three giant rats and must wait in fear for Megan and their mothers to save them.

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Sweet Stuff wants to play games with everyone else, but feels left out because she is an Earth Pony and doesn't seem to be good at anything. She ends up surprising everyone (even herself!) when she joins a treasure hunt with the pegasi and is the only one able to answer the last riddle and win the game!