A powerful sorcerer could be the main antagonist. Maybe the sorcerer is trying to gather all the meta - human powers for some dark ritual. He targets Beast Boy first because his power of transformation is unique and could be a key component in the ritual. So, he casts a spell that takes away Beast Boy's powers.
Maybe in the fanfic, there's a powerful villain who has a device that can nullify superpowers. Beast Boy gets caught in the range of this device and loses his powers. He struggles with feelings of uselessness at first. But then he realizes that his skills as a strategist and his knowledge of the Titans' operations are still valuable, and he uses those to help the team in a different way while also searching for a power restoration method.
Trigon could also be the main antagonist. Given his immense power and his connection to Raven, he could target Beast Boy as a way to get to Raven or simply to cause chaos among the Teen Titans. His demonic powers could be too much for Beast Boy to handle, ultimately resulting in Beast Boy's death.
It could be a power - hungry warlord in the story's setting. This warlord might be the one who ordered an attack on Carl's group, leading to Carl losing his eye.
The most obvious main antagonist could be the Other Mother. She is already a menacing figure in the original story. In a fanfic where Coraline loses the game, the Other Mother could use her powers to manipulate the game in such a way that Coraline has no chance of winning. She might change the rules mid - game or create illusions to deceive Coraline.
The main antagonist could be an old enemy who has resurfaced and is more powerful than ever. This enemy targets Naruto specifically and manages to injure him so severely that he loses his arm. For example, Orochimaru could return with new and more deadly powers.
It could be an old enemy who takes advantage of Percy's weakened state. For example, Kronos might see this as an opportunity to finally defeat Percy and take over Olympus. Since Percy has lost an arm, Kronos might think he's more vulnerable and launch a new attack.
It could be Orochimaru. He's always been interested in Naruto's power. Maybe he devises a plan to make Naruto lose his memory so he can manipulate him more easily, perhaps to use him as a weapon against the Hidden Leaf.
It could be Kaguya. If Kaguya were to return and use her powerful abilities to drive Naruto mad, perhaps by invading his mind with dark thoughts and memories. She has the power to warp reality and minds, so she could easily make Naruto lose his sanity. And since she has a grudge against the world of ninjas, making Naruto, one of the most powerful ninjas, go insane would be a great way for her to start her reign of terror all over again.
A new and mysterious dark ninja could be the main antagonist. This character might have a special ability to corrupt others. They target Naruto specifically because of his power and influence. By using some form of dark jutsu or psychological manipulation, they make Naruto lose his humanity, turning him into a weapon against the very people he used to protect.
It could be a new dark wizard who has a vendetta against Harry. This wizard might have created a spell specifically designed to target Harry's emotions, as he knows that Harry's strength often comes from his love and friendship. By taking away his emotions, he hopes to weaken Harry and make him easier to defeat.