Maybe an ancient Pokémon that has been in slumber for ages wakes up and realizes the importance of the Jewel of Life. So, it becomes the main character and embarks on a journey to safeguard it. This Pokémon could have unique powers that help it in this mission.
One possible plot could be that the Jewel of Life has been stolen from its rightful place. Arceus chooses a young and brave Pokémon or human to retrieve it. Along the way, the protagonist discovers the true nature and power of the jewel and has to face many challenges, like traversing dangerous terrains and outsmarting cunning enemies.
It could be Sam Fisher from Splinter Cell. He's a well - known and highly skilled agent. His experience in stealth operations would make him a great fit in the RWBY universe, where he could face new challenges like dealing with the Grimm while also using his skills to help the RWBY characters.
Allison could also be a main character. She has her own set of skills and a strong will. In the crossover, she could be the one who discovers the first signs of the connection between the Teen Wolf world and the Shuffle world. Maybe she's on a hunt in the forest near Beacon Hills and stumbles upon something that transports her to the Shuffle world, and then she has to find a way back while also uncovering the secrets of this new place.
Maybe a group of dark - type Pokémon that have banded together and are trying to overthrow Arceus. They view Naruto as an easy target at first, but quickly realize he is a formidable opponent with his ninja skills and new Pokémon - related powers. They would constantly try to undermine Naruto and his efforts to protect the Pokémon world.
Another possibility is a new character introduced specifically for this fanfic. This character could be an outsider to the RWBY world, coming from the world of the crossover. They find the single rose and have to navigate the RWBY universe while dealing with the power the rose gives them. It could be a really interesting way to explore both universes from an outsider's perspective.
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.
A powerful and ancient Pokémon from a long - forgotten era could be the cause. This Pokémon might have a grudge against Arceus for some past event and has finally found an opportunity to strike and hurt it. For instance, if Arceus had banished this Pokémon in the past, it could now be seeking revenge.
In the Naruto world, it could be Orochimaru. He might be interested in Naruto's newfound Pokémon - related powers and try to capture him to experiment on him. Orochimaru is always after power, and Naruto's unique abilities could be very appealing to him.
In a crossover with Snow White, the Evil Queen could be the main antagonist. She might be jealous of Tinkerbell's magic and try to capture her to use her pixie dust for her own dark purposes.
Obviously Naruto would be one of the main characters. And from 'The 100', Clarke would likely be a main character as well since she is a central figure in her own show.