Perhaps a power - hungry villain from Gwen's own world who sees the Omnitrix as a way to gain ultimate power. This villain might be someone who has been lurking in the shadows, waiting for an opportunity like this. They could try to manipulate Gwen or simply steal the Omnitrix from her. Another possibility is an alien race that sees the Omnitrix in the wrong hands (Gwen's in their view) and tries to take it back to where they think it belongs.
One possible antagonist could be an alien bounty hunter who wants to take the Omnitrix from Gwen for his own purposes.
In this fanfiction, the antagonists could be quite diverse. There might be a group of tech - savvy thieves who want to reverse - engineer the Omnitrix. They could target Gwen to get their hands on it. Additionally, there could be an old enemy of the Omnitrix's previous users who resurfaces when they sense the Omnitrix is active again with Gwen. This enemy could have a vendetta against anyone who wields the Omnitrix and would stop at nothing to destroy it, even if it means harming Gwen.
In this fanfiction, Gwen might use the Omnitrix to fight new and unexpected villains. She could transform into various alien forms and discover new powers within each transformation.
One possibility is that the story could explore how Gwen's personality changes when she has the Omnitrix. She might become more confident or more responsible. Also, there could be new villains who are attracted to the Omnitrix now that Gwen has it. She would then have to face these threats and protect the Omnitrix from falling into the wrong hands.
The story could start with Gwen unexpectedly getting the Omnitrix. Then, she might start exploring the different alien forms she can transform into. She'd likely test out their powers in various situations, gradually getting a handle on how to use them effectively.
Another option is a group of demons who have a vendetta against Clary or the shadowhunters in general. They might use torture as a way to break her spirit and gain information about the shadowhunters' defenses.
Maybe there are some secret organizations that want to study the baby because it's a hybrid of Ben and Gwen's powers. These organizations might not have evil intentions at first, but their methods of trying to get the baby could make them antagonists as they go against Ben and Gwen's wishes to protect their child.
The antagonists could be forces of dark magic. They might sense the power within the baby and want to either corrupt it or use it for their own evil purposes. For example, there could be a sorcerer who wants to steal the baby and raise it to be his minion. Also, some neighboring kingdoms that see Camelot's new heir as a future threat might send spies or assassins to target the baby.
Well, he'd probably be super OP. He could transform into all kinds of alien forms and use their powers in his battles. Imagine Naruto using Heatblast's powers to fight against Akatsuki members. It would be a whole new level of combat in the Naruto universe.
One possible storyline could be that they face a lot of family drama. Their families might be shocked and have different reactions, some may be supportive while others are against it. It could also explore how Ben and Gwen deal with the sudden responsibility and how it changes their relationship from just being cousins to co - parents.
Perhaps it could be a group of bullies from Issei's school days. They used to pick on him and now he's coming back to make them pay.
Hawkmoth is usually the main antagonist. Since he is the one who akumatizes Marinette in the first place. He takes advantage of her negative emotions, like her insecurities or anger, to turn her into an akuma and use her for his own evil plans.