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.
Furbob is afraid of the Stonebacks, but Megan convinces him that they are friends, not enemies.
The Little Ponies prepare for a "Welcome Back" party for their human friend, Megan. Meanwhile, little furballs called Bushwoolies are the slaves of a feline witch named Catrina and are watched over by a shape-shifting lizard named Rep. When the Bushwoolies escape, Catrina abducts Baby Moondancer and the Rainbow of Light to force the ponies to be her new slaves.
Megan and the others come to free the Flutter Ponies, but end up captured themselves!
