Dark Matter could be the main antagonist in this crossover. Dark Matter is a powerful and menacing force in Kirby's world. In the crossover, it could have somehow found a way to cross over into Sonic's world and is corrupting it. Sonic and Kirby have to find a way to stop Dark Matter from spreading further. Dark Matter tries to use Sonic's speed against him by creating dangerous obstacles in his path and Kirby has to use his various powers to help Sonic overcome these while also directly fighting Dark Matter.
Eggman Nega could be a great main antagonist. He has the intelligence and the desire for power. He could find a way to open portals between the Sonic X and Sonic Boom universes to steal resources and technology from both. His plans would force Sonic X's Sonic and Sonic Boom's Sonic to team up against him. He could use his robotic creations from both universes, combining the advanced tech from Sonic X and the more rustic, yet effective, machines from Sonic Boom.
A brand - new character could also work well. Imagine a powerful sorcerer from a different dimension. This sorcerer has the ability to manipulate time and space, which would put both Shadow and Silver at a disadvantage. He could be after Sonic's chaos emeralds to increase his own power and spread his dark magic across all the Sonic universes.
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.
It could be Dr. Robotnik teaming up with the Fratellis. Dr. Robotnik might see the potential in the Goonies' treasure or the area they live in for his own evil plans. He teams up with the Fratellis who are already villains in the Goonies' world. Together, they create chaos and try to stop Sonic and the Goonies from achieving their goals, whether it's protecting the treasure or saving Sonic's friends.
Dr. Eggman could be a likely main antagonist. He might team up with some of Mega Man's foes, like Dr. Wily. Together, they could create a super - weapon that combines Eggman's mechanical monstrosities with Wily's robotic minions. Their goal could be to take over both Sonic's and Mega Man's worlds.
One possible plot could be that an evil force is threatening both Kirby's and Sonic's worlds. They accidentally cross paths while investigating strange happenings. Kirby can use his ability to copy powers and Sonic can use his speed to explore different areas. Together, they combine their skills to defeat the common enemy. For example, Kirby might copy Sonic's speed ability for a short time, allowing him to quickly reach parts of the battlefield that Sonic couldn't access alone. And Sonic could use Kirby's star power to enhance his own attacks.
Sonic would definitely be one of the main characters. His speed and heroic nature would make him a key figure in any crossover. Also, Freddy Fazbear from FNAF would be important as he is sort of the face of the FNAF franchise. Sonic could be the one trying to find a way out of the FNAF world or stop the animatronics, and Freddy could be the character that Sonic has to either defeat or befriend in order to achieve his goal.
Obviously, Star Dream itself could be the main antagonist. It's a powerful and somewhat unpredictable machine. It might have its own motives that conflict with Kirby's, like wanting to control all of Pop Star for some unknown reason.
The Riddler could be a great main antagonist. He could use his intellect to create puzzles and traps that not only challenge Batman's detective skills but also the Flash's speed. For example, he could set up a series of time - locked puzzles where the Flash has to use his speed in a very specific way at specific times to unlock them, while Batman has to figure out the overall pattern of the puzzles.