Maybe a corrupted version of a major character from either universe could become the villain. For instance, if a Sailor Scout was corrupted by the dark magic from SVTFOE, she could turn against her friends and start causing chaos. Or if Marco was somehow influenced by the negative energy from Sailor Moon's world, he could become a threat. This would add an interesting layer of drama and betrayal to the crossover fanfiction.
A new character could be created as the main villain. This villain could be a powerful sorcerer who has studied the magics of both Sailor Moon and SVTFOE. He discovers a way to merge the two universes in a way that benefits him but is harmful to everyone else. He might try to control the Sailor Crystals and the magic of SVTFOE at the same time. To stop him, the characters from both universes would have to put aside their differences and fight together.
One idea could be that the Sailor Scouts somehow end up in the SVTFOE universe. They could team up with Star and Marco to fight a common enemy. Maybe an evil force that combines the darkness from both universes.
It could be an evil sorcerer who has the power to steal chakra and magical energy. He plans to use this stolen power to reshape both the Naruto and Sailor Moon universes according to his own dark desires. He's able to create powerful illusions that fool even the most experienced ninja and senshi, making him a very difficult enemy to face.
The Dark King from Sailor Moon could team up with the Volturi. The Dark King's thirst for power combined with the Volturi's strict vampire laws could create a really menacing force. They could be trying to take over both the magical world of Sailor Moon and the vampire - filled Twilight world.
A corrupted spirit that was once a guardian of the Underworld but has been twisted by jealousy or a thirst for power. This spirit sees the Sailor Guardians as a threat to its newfound plans of domination. It uses its knowledge of both the Underworld and the weaknesses of the Sailor Guardians to try and defeat them. It might also try to turn some of the underworld creatures against the Sailor Guardians.
Maybe a corrupted version of one of the Sailor Scouts. She could be jealous of Naruto's attention towards the other Scouts in the harem. So, she makes a deal with a dark force from Naruto's world, like a powerful Orochimaru - like character. This combined power of dark jutsu and a twisted Sailor power would create a very interesting and complex main antagonist for this crossover fanfiction.
Well, in such a fanfiction, the art styles could be blended in an interesting way. The Sailor Scouts could have a new look inspired by Batman's aesthetic, like darker colored fuku with bat - like symbols. And Batman could get a touch of Sailor Moon's magic, perhaps his utility belt having some magical items. The story could explore how two very different universes collide, and how the characters grow from the experience.
Well, one possible plot could be that the Sailor Scouts are transported to the Pokemon world. They might team up with some Pokemon trainers to fight against a common enemy. Maybe an evil organization is trying to use both the power of the Dark Kingdom from Sailor Moon and some powerful, dark Pokemon. The Sailor Scouts' magical powers could interact in interesting ways with the Pokemon's abilities.
Well, perhaps Voldemort teams up with some of Sailor Moon's villains. Harry and Sailor Moon then have to put aside their differences in fighting styles and beliefs to take on this combined evil. The Sailor Scouts could teach the Hogwarts students about their powers of love and friendship, which could be a new concept in the wizarding world. And Harry could show them how to use magic in more creative ways in battle.
A Sailor Moon and Dragonball Z crossover fanfiction might start with a strange rift in the universes. Sailor Mercury detects an unusual energy signature that seems to be a mix of magic and ki. As they investigate, they run into Goku who is also curious. The two groups then find out that there's a powerful being trying to merge their worlds for its own evil purposes. The Sailor Guardians and the Z - fighters would then have to put aside their differences in fighting techniques and beliefs to stop this threat. They might have some funny moments like Vegeta getting annoyed with Sailor Mars' sassy attitude or Sailor Venus being in awe of Goku's strength.
Maybe the NCIS team stumbles upon a strange artifact that has the power to open portals to different dimensions. Unknowingly, they activate it and end up in the world of Sailor Moon. There, they meet Sailor Moon and her friends who are in the middle of a battle against the forces of evil. The NCIS agents, with their knowledge of forensics and combat skills, offer their help. In return, the Sailor Scouts teach them about the magic and powers in their world. Together, they form an unlikely alliance to defeat the common enemy.