A possible plot is that Discord decides to hold a 'discordance' competition in Equestria. The ponies, at first reluctant, get into the spirit. But things go too far when he starts changing the rules mid - game. The MLP characters then have to find a way to end the competition on their terms while still keeping Discord entertained. Or perhaps Discord gets bored and decides to swap the personalities of all the ponies. Pinkie Pie becomes super serious and Twilight becomes overly giggly. The story could be about how they deal with these new personalities and get back to normal.
Well, a plot could revolve around Discord creating a parallel universe where all the MLP rules are reversed. Ponies fly backwards, magic works in strange ways, and the day - night cycle is all messed up. The MLP characters have to journey through this strange world to find Discord and convince him to put things right. Another idea is that Discord invites some of the MLP characters to his chaotic realm for a party. But once they're there, they realize they have to complete a series of crazy challenges to get back home.
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.
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 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.
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.
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.
Definitely Twilight Sparkle. Her studious nature and powerful magic would create an interesting dynamic with Discord's chaos. She'd be constantly trying to analyze and fix whatever Discord has messed up. Pinkie Pie is also great. Her zany personality could either match Discord's chaos or be a source of irritation for him. Rainbow Dash would be cool too. Her bravado and flying skills could be put to the test when Discord throws up some wild obstacles in her path.
A plot could also revolve around her discovery of her heritage. Maybe she starts off not knowing who her father is and as she uncovers the truth, she has to come to terms with being the daughter of such a chaotic being. This internal struggle could be a major part of the fanfic.
One interesting aspect is the unique character dynamics. Discord is a chaotic character, and in a fanfic centered around his 'bride', it can lead to really unexpected and humorous interactions. For example, his attempts to court in his own chaotic way can be both funny and endearing.
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 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.