It could be a rogue scientist who was once part of the Gundam project. He has his own ideas about how the Gundam technology should be used and is willing to do anything to get his hands on it, even if it means going against Sonia and the Gundam's pilot.
Maybe an alien race that sees the Gundam as a threat to their plans of colonizing the planet. Sonia and the Gundam become the last hope to defend the Earth. The aliens have advanced technology and unique combat strategies, making them formidable antagonists.
One interesting Sonia x Gundam fanfiction could be about Sonia being a pilot in a new Gundam series. She might have to face tough battles and form a special bond with her Gundam unit. In this story, the relationship between Sonia and her Gundam could be explored, like how she customizes it to fit her combat style.
You can try fanfiction websites such as Archive of Our Own (AO3). It has a large collection of fan - created works, and there's a good chance you'll find Sonia x Gundam fanfiction there. Just use the search function and type in 'Sonia x Gundam' to see the available stories.
It could be a future version of someone who has turned evil due to Shinn's time - traveling actions. For example, if Shinn changes something that causes a once - good character to go down a dark path. Maybe a character who was originally a minor figure in the original story but becomes a major threat because of the altered timeline.
One idea could be that Sonia discovers a hidden power within the Gundam that only she can unlock. This power could be the key to saving their world from a new, powerful enemy.
One option could be Kaguya from the Naruto universe. Her god - like powers would pose a great threat to Bayonetta. She could be trying to expand her influence into Bayonetta's world, seeing it as a new place to conquer.
It could be a dark wizard who wants to capture the nymph for her powers. He sees the nymph's connection to nature and wants to use it to gain ultimate power in the Naruto world.
It could be a rogue ninja who has also discovered a way to harness the power of Amaterasu in a corrupt way. This ninja might want to use the power to take over the ninja villages and Naruto stands in his way.
It could be a new character who has the ability to disrupt both Lambo's time - traveling powers and the Reborn characters' mafia - based powers. This antagonist might be after a powerful artifact that Lambo and the Reborn crew are protecting.
It could be an evil ninja from Naruto's world who has somehow gained the ability to control Digimon. He wants to use this power to rule over both worlds. He targets Renamon because of her connection to Naruto and tries to break their bond. He might also be after the special powers that Naruto and Renamon possess when they work together.
It could be a rogue ninja who has a vendetta against Naruto and sees Heather as a way to get to him. Maybe this ninja was once defeated by Naruto and now wants to use Heather as bait or hurt her to break Naruto's spirit.