A possible plotline is centered around a mystery that spans both universes. Maybe there are artifacts in both the Fate and Mahouka worlds that are somehow connected. Characters from both sides would then have to work together to uncover the secrets behind these artifacts. This could lead to some interesting character interactions, as the values and abilities of the Fate characters and the Mahouka characters are quite different. They would have to learn to trust each other and combine their skills to solve the mystery.
I think a pairing between Shiba Tatsuya from Mahouka and Archer from Fate would be really interesting. Tatsuya is a very powerful and intelligent magician in his own right, and Archer has a wealth of combat experience and a complex personality. They could have some great philosophical debates about the nature of magic and the purpose of their powers.
Maybe the fanfic focuses on a single character, like Marle, who realizes that her fate is to be a pawn in a greater political game. So she starts a journey to rewrite her own fate and in the process, she uncovers secrets about the Chrono Trigger world that no one knew before. This could involve her making alliances with unlikely characters and using her unique abilities in ways that were not explored in the original game.
One possible plotline is that Ben Tennyson accidentally gets transported to the world of Fairy Tail. He has to figure out how to use his Omnitrix in a world full of magic. Another could be that the Fairy Tail guild discovers an alien device similar to the Omnitrix and they try to figure out how it works.
One possible plotline could be Naruto somehow obtaining the powers of Doctor Fate and using them to protect the Hidden Leaf in a different way. Maybe he uses Doctor Fate's magic to fight against threats that normal ninja techniques can't handle.
A possible plotline could be that the Ghost Rider's power somehow leaks into the Vampire Knight world. For example, a strange portal opens and the essence of the Ghost Rider enters Cross Academy. This causes chaos as the vampires and vampire hunters are affected in different ways. Some vampires might be weakened by the holy fire aspect of the Ghost Rider, while some hunters might gain new powers. The characters then have to figure out how to close the portal and restore balance.
One possible plotline could be the characters from Kekkai Sensen getting involved in the Holy Grail War from Fate. Maybe they are summoned as Servants or they interfere with the war for their own reasons. Another could be the Fate characters ending up in the world of Kekkai Sensen and having to deal with the strange creatures and the kekkai barriers there.
A really interesting plotline could be about the discovery of the connection between Fanalis and Saiyan powers. Maybe there's some ancient prophecy or hidden knowledge that links the two species. The story could then follow the characters as they uncover this mystery and what it means for their respective worlds. There could also be a plotline where a group of Fanalis and Saiyans team up to face a common enemy that threatens both of their existences, leading to some epic team - up moments and character development as they learn to work together.
One interesting concept is the combination of different Fate series characters in unexpected scenarios. For example, seeing characters from Fate/Stay Night interact with those from Fate/Grand Order. It can create unique storylines and character dynamics.
One possible plotline could be that Vincent, with his dark past and combat skills, gets involved in Negi's magical world. Maybe he helps Negi in a battle against a powerful dark magic user.
One possible plotline could be that an evil force is threatening both the Miraculous Ladybug world and the Voltron universe. So, Ladybug and Chat Noir are called upon to help the Voltron paladins. They have to learn how to use their powers in this new universe and also figure out how to combine their powers with Voltron's. Another plotline could be that a character from one universe accidentally ends up in the other. For example, Pidge could end up in Paris and meet Ladybug and Chat Noir. She could then try to find a way back home while also helping them fight Hawk Moth.