Another option for the main antagonist could be Blocky. Blocky is often a bit of a troublemaker in the BFDI series. He might see Pen and Pencil as a threat to his own status or he could just be bored and decide to make their lives difficult. He could constantly set up traps or challenges specifically designed to target Pen and Pencil's weaknesses.
It could be Eraser. Since Pen and Pencil are the main characters, Eraser might be jealous of their new - found friendship or relationship. Eraser could try to break them apart by causing misunderstandings or directly interfering in their tasks and challenges within the BFDI world.
The main antagonist could also be an outsider object that enters the BFDI world. This new object might have a different ideology and see Pen and Pencil's bond as something that goes against the rules or norms of the world. So, it tries to disrupt their relationship and create chaos in the BFDI world in an attempt to force them apart.
One possible plot could be that Pen and Pencil are in a competition within the BFDI world. They start off as rivals, constantly trying to outdo each other in various challenges. But as the story progresses, they realize that they can achieve more by working together. They then form an alliance and use their unique abilities (like Pen's writing and Pencil's erasing in a metaphorical sense) to overcome the other contestants and reach their goals.
Common themes in BFDI pen x pencil fanfiction often revolve around their individual abilities. For example, the pen's ability to write in a more permanent way and the pencil's ability to be erased. This can lead to stories about how they deal with mistakes. Another theme could be loyalty. Are they loyal to each other? Do they stay true to their friendship? And sometimes, there are themes of self - discovery. As they interact with other characters in the BFDI world, they might discover new things about themselves and their relationship with each other. For instance, they might realize that they are stronger together than apart.
Well, you can try searching on some fanfiction platforms like Archive of Our Own. There might be various stories there that explore the relationship between pen and pencil in the BFDI universe. Just type in the relevant keywords and browse through the results.
It could be Orochimaru. He's always been interested in unique powers and abilities. The idea of X - 23's mutant abilities and Naruto's jinchuriki powers would be very appealing to him. He might try to capture them both to use in his experiments to gain ultimate power.
Maybe an evil sorcerer from a third, unknown dimension who sees the potential in both Naruto's chakra and Pneuma's power. He plans to steal their powers to become invincible. He starts by creating unrest in both their worlds, pitting their friends and allies against them. Naruto and Pneuma must figure out his true identity and stop him before he succeeds in his devious plan.
It could be an evil ninja who has somehow gained access to the technology from Neo's world and wants to use it to take over the Naruto world. He might be able to create clones using digital technology, making him a very difficult enemy to defeat.
A new, mysterious organization that wants to control the chakra of strong ninja could be the main antagonist. They see Inojin and Himawari as prime targets due to their unique abilities. The organization would try to capture them, which would force Inojin and Himawari to fight together and also test their relationship as they face this powerful threat.
An old rival of Dino's from his past could show up. This person might have a grudge against Dino and decides to target Hibari as a way to get to Dino. Since Hibari is so proud and strong - willed, he doesn't take kindly to being used as a pawn, and together with Dino, they have to face this old enemy. This antagonist could have some powerful fighting abilities or some dark secrets that make it difficult for Dino and Hibari to defeat him.
Dr. Eggman could be a great antagonist. He might be creating a new weapon or device that could disrupt the balance between time (which is relevant to Silver) and space (relevant to Shadow). His actions force Silver and Shadow to work together to stop him.
An ancient evil entity that has awakened and sees Ulbert and Demiurge as a threat to its domination. This entity could have powers that are difficult for them to counter, and it uses psychological warfare as well as physical attacks. For instance, it might try to corrupt Demiurge's loyalty or make Ulbert doubt his own abilities.