It could also be a new character, perhaps a powerful and evil wizard from a forgotten zone. This wizard could be trying to spread chaos and destruction in the Sonic world, and Antoine stands in his way.
It could also be a new villain that is specifically interested in Sonic because she is now a girl. Maybe a villain who has some sort of vendetta against female heroes or wants to use Sonic's new form for some evil experiment. However, Dr. Eggman is so iconic in the Sonic series that he would be a strong contender for the main antagonist role even in this fanfic scenario.
Maybe a new character could be the main antagonist. This character could be jealous of Sonic's speed and popularity. So, when Sonic turns into a girl, this antagonist sees it as a chance to frame Sonic for various crimes in this new form. This would make Sonic's friends doubt him and isolate him, all part of the antagonist's plan to take Sonic's place as the hero of their world.
Dr. Eggman could be a great main antagonist. He could be using the chaos of war to further his own plans for world domination. He might be creating powerful war machines and using them to take over different regions, forcing Sonic and his friends to fight back to protect the peace.
A new character could be introduced as the main antagonist. For example, a being from another dimension who has been observing both Sonic's and Megaman's worlds. This being realizes that by combining the chaos energy from Sonic's world and the advanced robotics technology from Megaman's world, it can create a new, all - powerful empire. So it starts to manipulate events in both worlds to bring about this combination, while Sonic and Megaman have to stop it.
Dr. Eggman and Dr. Wily could team up. Dr. Eggman has his mechanical creations and knowledge of Sonic's world, while Dr. Wily is an expert in creating powerful robots in Mega Man's world. Together, they could be a formidable force against Sonic and Mega Man.
Well, obviously Dark Gaia itself could be the main antagonist. It has the power to cause chaos and destruction, and Sonic would have to stop it from wreaking havoc on the world.
Dr. Eggman would be a likely choice as he often causes trouble for Sonic. In the context of Secret Wars, he could have found a way to connect Sonic's world to other dimensions and start the wars to finally defeat Sonic once and for all. He might be using new and powerful machines he has created from the combined technology of different dimensions.
Dr. Eggman would be an obvious choice. Since Sonic is now in a more vulnerable human form, Eggman could see this as the perfect opportunity to finally defeat Sonic and take over the world. He might come up with new devious plans, like creating robots specifically designed to target a human Sonic.
Another possibility is a corrupted version of one of Sonic's friends. Maybe through some dark influence, like an evil Chaos Emerald, a friend turns on Sonic and blinds him. This would add an extra layer of drama as Sonic has to deal not only with his blindness but also the betrayal of someone he trusted.
Another plot could involve Antoine having to team up with an unlikely character. For example, he teams up with a villain who has a change of heart temporarily. Together they face a greater threat that endangers the whole Sonic universe. This would create an interesting dynamic between them as they learn to trust each other.