Maybe the main villain could be a mutated gremlin. In the fanfiction, this gremlin could be the result of some strange experiment within the Clamp Center. It becomes much larger and more powerful than the other gremlins and has a vendetta against Gizmo. It tries to gather all the other gremlins to follow its lead in causing maximum destruction.
It could be a corporate executive at the Clamp Center. He sees the gremlins as a way to make a huge profit. He starts to capture and sell gremlins on the black market. But in his greed, he accidentally releases a group of extremely dangerous gremlins that are out of control. He then becomes the main obstacle for Billy and Gizmo as they try to stop these gremlins from causing more harm, all while trying to expose the executive's illegal activities.
One possible plot could be that a new type of gremlin is accidentally created in a lab near the Clamp Center. This new gremlin has the ability to fly and is much smarter than the regular ones. The main character, Billy, has to team up with Gizmo again to find a way to stop this new threat before it takes over the city.
It could be a speedster from another universe who has come to challenge Flash. This villain might have some unique powers related to speed that Flash has never encountered before, like the ability to steal speed from other objects or people.
In a new Ash Unova fanfiction, the main villain could be a scientist who is conducting unethical experiments on Unova Pokémon. He believes that by fusing different Pokémon together, he can create the ultimate Pokémon. His experiments are causing harm to the Pokémon involved and are also disrupting the natural balance in the Unova region. Ash discovers what's going on and has to stop the scientist, not only to protect the Pokémon but also to save the Unova region from the potential disasters that could be caused by these abnormal Pokémon creations.
A powerful wizard from a forgotten dimension could be the new villain. He sees Seabrook as a place full of unique energy that he can use to gain more power. He starts by creating chaos among the zombies, aliens, and humans, using his magic to turn them against each other.
A jealous show - dog breeder could be the new villain. He sees the Dalmatians getting all the attention and decides to plot against them. He tries to frame them for causing chaos at dog shows so that his own dogs can win all the prizes.
A possible main villain could be an ancient sorcerer from the new dimension who has been awakened from a long slumber. He's enraged that the wizarding world has been interfering with his dimension's magic, and decides to take revenge on Harry Potter's world. He has powers that are unknown to the normal wizarding world, like the ability to control time in his dimension, which makes him a formidable foe.
A corrupt politician could be the new villain. He uses his power and influence to cover up his illegal activities, like embezzling funds meant for the city's development. The Punisher would see through his lies and decide to take him down.
It could be a long - lost relative of Voldemort, carrying on his dark legacy.
A tech - genius who was once a protégé of Tony Stark but turned against him out of jealousy. He creates his own army of robotic suits.
I don't know for sure since I don't have the details of this 'gremlins first story'. It could be a human protagonist who discovers the gremlins.