Maybe the dark wizard gets accidentally transported to the MLP universe and has to figure out how to get back. Along the way, he forms an unlikely friendship with one of the ponies who tries to help him, but he also has his own dark motives hidden. This creates a lot of internal and external conflict.
A possible plot could involve the dark wizard using his dark magic to corrupt some of the ponies in Equestria. The main characters in MLP then have to find a way to stop him and reverse the corruption. They might need to seek help from other magical beings in their world or even discover new powers within themselves to combat the dark wizard's magic.
One idea could be that the dark wizard tries to steal the magic of Equestria in the MLP world. He might be lured by the pure and powerful magic there.
One idea could be that the ponies from MLP accidentally enter the Pokemon world through a magical portal. They team up with some Pokemon trainers to stop an evil team that's trying to use both pony magic and Pokemon power for their own bad deeds. Another plot could be a Pokemon tournament where ponies are allowed to participate using their unique abilities as if they were Pokemon. For example, a Pegasus pony could use its flying skills in a battle like a Flying - type Pokemon.
One idea could be that Discord causes chaos in Equestria that the MLP characters have to solve in a really wacky way. For example, he might turn all the clouds into cotton candy and the ponies have to figure out how to make it rain again without making a huge mess. Another plot could involve Discord getting his powers mixed up with a unicorn's magic and they have to work together to undo it. Maybe he accidentally gives Twilight Sparkle the power to turn things into random objects every time she tries to use her normal spells.
Another plot could involve a villain that is a threat to both worlds. The Fairy Tail wizards and the MLP ponies would have to team up to defeat this common enemy. Maybe the villain is stealing magic from both worlds to become all - powerful. The ponies with their unique abilities and the wizards with their powerful spells would combine their forces in an epic battle.
Maybe there's a villain from the MLP world that follows them into the Equestria Girls world. The girls then have to team up with their Equestria Girls counterparts to defeat this villain. They could combine their different skills, like the pony Rainbow Dash's speed in the air and the Equestria Girls Rainbow Dash's skills on the track team.
Well, in an MLP Dark Mirror Universe fanfic, a possible plot is that the Elements of Harmony are actually used for evil. The ponies who usually protect Equestria are now using the power of the elements to control and oppress others. There could also be a plot where the different pony races are at war with each other instead of living in harmony. Maybe the unicorns think they are superior and are trying to enslave the earth ponies and pegasi. And of course, the fanfic could explore how the friendships that were once strong in the normal Equestria are now broken in this dark mirror world.
Perhaps there is a portal that connects Cybertron and Equestria. Some ponies accidentally end up on Cybertron and are shocked by the mechanical world. The Transformers have to help them get back home. Meanwhile, some Autobots are curious about the ponies' world and decide to accompany them. This leads to a cultural exchange of sorts between the two groups, with lots of misunderstandings at first but then growing respect and friendship.
One idea could be Discord causing chaos in Equestria that only the Mane 6 can stop with their unique friendship powers. For example, he might mix up the elements of harmony, and the ponies have to go on a quest to put them back in order while dealing with Discord's wacky challenges.
One interesting aspect might be the character interactions. Picture Captain Kirk trying to charm the ponies or Spock having deep philosophical discussions with Twilight Sparkle about the nature of existence. The different cultures in Star Trek, such as the Klingon warrior culture, could also contrast with the peaceful pony society. This could lead to some really unique storylines where the ponies have to deal with more aggressive or complex beings, and the Star Trek characters have to adapt to the more harmonious and magical environment of Equestria.
One idea could be that the ponies from MLP accidentally end up in Gravity Falls. Twilight could be intrigued by the strange anomalies in Gravity Falls and try to study them with Dipper's help. Maybe Pinkie Pie's party - planning skills could be used to liven up Gravity Falls' rather spooky events.
Twilight Sparkle could be a great main character. She is very knowledgeable about magic in the MLP world. Facing a dark wizard would test her skills and knowledge to the limit, and she could learn a lot from this encounter.