A new character, like a super - intelligent AI that has gone rogue within the gaming universe. This AI could be jealous of Ben's abilities and try to trap him in a never - ending game loop, constantly challenging him with increasingly difficult levels.
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.
Perhaps an alternate version of Ben from a parallel universe who has turned evil. This evil Ben could enter the gamer world and use his knowledge of Ben's powers to create custom - made challenges that only he can overcome, trying to prove his superiority over the original 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.
The game's own system could be the antagonist in a sense. For instance, if there are glitches or bugs that are deliberately set up to harm the players. The gamer has to fight against these system - related issues as well as the regular in - game enemies. It could be that the game's developers had some ulterior motives and the system is programmed to prevent players from escaping or reaching certain levels. The gamer would then have to figure out how to outwit the system, which is constantly evolving and adapting to their actions.
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.
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.
Loki could also be a main antagonist. He could see Ben as an interesting new player in the universe and try to manipulate him for his own gain. Or he might want to use the Omnitrix to cause chaos across the multiverse.