There could be a new entity created from the merging of the darkest parts of both universes. This entity is interested in chaos and destruction. It sees Naruto and the Sailor Scouts as threats to its plans. It has the ability to use some of the most dangerous jutsu from Naruto's world and also manipulate the negative energy in the Sailor Moon world. The entity would be a great antagonist as it forces Naruto and the Sailor Scouts to combine their different powers and strategies to defeat it.
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.
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.
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.
Obviously Sailor Moon herself. Her kind - hearted and brave nature would make her a great addition to the harem. And also Sakura from Naruto. She's strong - willed and has a long - standing relationship with Naruto that could develop further in this fanfiction.
It could be an old enemy of Kushina's who was thought to be dead but has now returned. Maybe someone from her days in the Uzumaki clan who has a vendetta against her and now sees Naruto as an obstacle too.
The main antagonist could be a combined form of Kaguya from Naruto and Elizabeth Greene from Prototype. Kaguya's god - like powers combined with Greene's virus - based abilities would make for a truly terrifying foe. She could be trying to merge the two worlds into one chaotic mess where she can rule supreme, using the shinobi's chakra and the virus - infected creatures to her advantage.
Tuxedo Mask could also be in the harem. He has a long - standing relationship with Usagi, and in a harem scenario, his feelings for her could be even more intense, competing with others for her love.
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.
Maybe the main antagonist is an artificial intelligence on the Clockwork Planet that views Naruto and his chakra abilities as a threat to its control over the planet. It starts to send mechanical beasts to Naruto's world to capture him and study his powers. This AI is highly intelligent and has a vast network of clockwork devices at its disposal, making it a formidable foe for Naruto and his friends.
One interesting plot could be that the Sailor Guardians are on a mission to a world similar to Naruto's. There, they meet Naruto and his friends. Naruto is initially confused by their strange powers but quickly realizes they can help fight a common enemy. Maybe an evil force from the Sailor Moon universe has teamed up with Orochimaru. The Sailor Guardians' magic combined with Naruto's ninja skills could make for some epic battle scenes.
One interesting plot could be that the villains from both universes team up. The Akatsuki from Naruto and the Dark Kingdom from Sailor Moon might join forces to collect powerful artifacts. Naruto and the Sailor Scouts would then have to put aside their differences in fighting styles and powers to defeat this new, combined threat. They could learn from each other's combat techniques. For example, Naruto might teach the Scouts about his shadow clone jutsu, while Sailor Moon could show Naruto how to use the power of love and friendship in a more direct way to boost his power in battles.