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.