A mutated Highbreed could be the main antagonist. This Highbreed was accidentally exposed to some other alien energy source that made it extremely powerful and insane. It views Ben's new Highbreed form as a rival and wants to prove that it is the superior Highbreed. It starts attacking planets and Ben has to stop it while still getting used to his own transformation.
It could be an evil Highbreed scientist. This scientist might be obsessed with creating a new breed of Highbreeds that combines the power of the Omnitrix with their own genetic superiority. He sees Ben as the perfect test subject for his experiments and will stop at nothing to achieve his goals.
Maybe a rogue Highbreed warlord. This warlord has his own plans for galactic domination and sees Ben's transformation into a Highbreed as a threat to his plans. He tries to either kill Ben or use him for his own purposes. The warlord could have a powerful army and advanced technology at his disposal.
Well, it could be about Ben getting an unexpected Highbreed transformation. Maybe he's on a mission and somehow gets exposed to some strange Highbreed energy. Then he has to deal with new powers and also the fact that he looks like a Highbreed, which might make his friends and enemies view him differently.
Vilgax could be a great antagonist. He could hack into the gaming systems to try and defeat Ben in a virtual world where the rules are different. He might use his advanced technology to create digital versions of his minions to attack Ben.
It could be a new alien species that Ben has never encountered before. This species could be territorial and see Ben as a threat to their planet where he's stranded. They constantly try to drive him away or capture him, which makes it difficult for Ben to find a way to leave.
One option could be an alien scientist who is obsessed with the power of the Nemetrix. He wants to study it and use it to create his own super - weapons. He might be from a race that has been at odds with the creators of the Nemetrix for centuries.
Maybe a malevolent scientist who has a grudge against female heroes. He believes that only men should have such powers and sets out to take the Omnitrix from Ben and use it for his own evil purposes. He underestimates Ben because she is a girl but soon realizes his mistake.
Ben Tennyson himself is often very popular in Highbreed fanfics. He's the main character of the Ben 10 series, so it's natural that he plays a major role. Writers like to explore his interactions with the Highbreed, whether it's in battle or in attempts at diplomacy.
Another possibility is that an alien race that Ben has previously encountered and thought was friendly, now turns against him/her because of the change in gender. They might have some strange beliefs or customs that make them view Ben's new form as a threat or an abomination, and thus they become the main antagonists in the fanfic.
Vilgax could be a great main antagonist. He has a long - standing feud with Ben and his appearance would immediately up the stakes. He could also manipulate Kevin into turning against Ben for a while.
Perhaps the main antagonist could be a former ally of Ben who has turned bad. After dawn, this character reveals their true intentions and starts causing trouble for Ben. They might have some sort of grudge against Ben or be power - hungry and see the Omnitrix as a means to gain ultimate power. They could use their knowledge of Ben's abilities and weaknesses to their advantage.
It could be an alien bounty hunter. This bounty hunter has been hired to capture Ben in his stuck - as - alien form. The hunter might have some special gadgets or powers that make it difficult for Ben to escape. And he's not interested in Ben's well - being, just in getting the reward for bringing him in.