A musical - themed villain could be interesting. This villain uses 3D sound waves as weapons and creates hypnotic music to control people in the Spy Kids' world. The Spy Kids would have to break the spell of the music and find a way to silence the villain's dangerous tunes.
Maybe the Spy Kids are shrunk down to a microscopic size in their 3D world. They must navigate through a world of tiny threats and find a way to reverse the process while also uncovering a plot by a mad scientist who wants to use their miniaturized state for his own evil experiments. Well, this would add a whole new level of adventure and danger to their spooky world of espionage.
The new villain could be a former student of the Nutty Professor who felt wronged in some way. Maybe the student was expelled unfairly (in his mind) or didn't get enough credit for his contributions to a project. So, he decides to seek revenge on the professor by using his own knowledge of the professor's research to create chaos in the university and in the professor's personal life.
A voodoo priestess who is using the zombies to carry out her revenge on the islanders for past wrongs.
The main villain could be an escaped criminal who stumbles upon the house thinking it would be a good place to hide. But when he realizes there's a kid alone, he decides to take advantage and ransack the place. The kid has to use his wits and the resources around the house to defeat this dangerous villain.
One option could be a rogue agent from within Shield who has turned against the organization. This agent could be jealous of Hawkeye's newfound status in Shield and tries to undermine him at every turn while also planning some sort of major heist or attack on Shield's assets. They might have some sort of high - tech weaponry that Hawkeye has to outwit with his arrows.
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.
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.
In some cases, it could be the environment itself. For instance, if they are in a highly dangerous and unforgiving area, like a collapsing building or a toxic zone, and Ellis makes a wrong move trying to lead the group through, which leads to his death.
A dark demigod who was once rejected by the gods and now wants to use the Staff of Fire to take revenge. He could be really powerful and have the ability to control shadows, using them to his advantage against Percy and his friends.