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Here is my list of made-up Season 6 episodes. These are just random ideas. 

Foal Of Cuteness

Twilight accidentally casts a spell on Ponyville, turning everyone into babies. She tries to find a spell that will change everyone back to normal.

Ponyzoid Sightings

Rumors go around about alien ponies coming to Ponyville. The rumors became true, as Ponyzoids come to Ponyville. The girls find a way to keep them out of town.

Another Magical Mystery Cure?!

The girls have their cutie marks switched.

The Fictional Mess-Up

Little Red Riding Filly, the Giant Stallion, and the Three Little Colts mysteriously escaped from their storybooks.

Evil Elements Of Harmony

The girls encountered their male evil equivalents.

My Little Party Pony

Pinkie's long-lost little brother comes to visit.

Every Picture Tells A Story

The girls speak about their past.

Get Over It

Rainbow Dash is tired of Fluttershy being a scaredy-pony. So she attempts to help her to be brave.

Go Bananas

Pinkie tries to forget about her embarrassing accident at one of her parties, but she ends up losing her mind.

Stallion That Laid The Golden Egg

Rarity's long-lost rival, Shard, comes to visit. He has been a real nuissence to her, until she realizes her mistake of driving him away.

Barking Up The Wrong Pony

Someone ate Pinkie's special homemade cupcakes and she is on the case. But she accused and puts the wrong pony in trouble.

Unsocial Butterflies

Fluttershy babysits her three young brothers. Two out of the three are not pegasi. The older one is an earth pony and the other is a unicorn. All three little colts are shyer than their older sister. Fluttershy attempts to help her little brothers interact with other foals.

Ponyzoid Harmony, Part 1

The King of the Ponyzoids has nightmares of a fireball-like pony plaguing him, and he searches for answers as to why the visions are haunting him.

Ponyzoid Harmony, Part 2

When the King of the Ponyzoids discovers a phantom star will collide with Ponyville, he orders his son to help the girls try to rid of it. With the help of the princesses' magic, the prince of the Ponyzoids deflects the star. Peace returns back to Ponyville, and the prince is now the new element of Harmony; Heroism.