It could be Chandler. He's always been a bit of a bully in the Loud House universe. With Lincoln having powers, Chandler might become jealous and try to find a way to take those powers away or use them for his own bad purposes.
Perhaps a new character could be introduced as the villain. A mad scientist who wants to study Lincoln's powers and will stop at nothing to get his hands on him. This scientist could create all sorts of dangerous contraptions to try and capture Lincoln.
There's also the possibility that one of Lincoln's sisters, if affected by some strange force, could turn into a villain. For example, if Luna got possessed by an evil spirit that made her jealous of Lincoln's powers, she could become a formidable adversary. However, in the end, Lincoln would surely try to save her and restore her to normal.
One possibility is that Lincoln could get super strength. He might use this power to protect his family from various threats in Royal Woods. For example, he could stop a runaway car that was about to hit his sisters.
It could be an evil scientist. This scientist was conducting experiments to create superhumans, but his experiments went wrong. Now, he's jealous of Marco's natural - born powers. So, he tries to capture Marco and study him to find a way to replicate his powers for himself. The scientist creates all kinds of dangerous traps and robotic minions to try and catch Marco.
There could be a new character in the fanfiction, like a bully who targets Lincoln just because he seems like an easy target and ends up hurting him.
The shooter could be a main character. We could explore their motives, their background, and what led them to commit such a heinous act. For example, if the shooter was a disgruntled former soldier who felt Lincoln had wronged him in some way. Another character could be Lincoln's wife. We could see her reaction, her grief, and how she copes with the situation. Or perhaps a doctor who tries desperately to save Lincoln's life could be a main character, showing the medical challenges and the hope against all odds.
His sisters could be main characters. For instance, Lori might give him some advice on how to deal with the braces since she's the eldest and has more experience. Or Leni could be there to offer some fashion tips to make him feel better about his new look with the braces.
Maybe in a fantasy fanfiction, an evil sorcerer is the villain. Christy might be a key figure in a prophecy to save the kingdom. So, the sorcerer tries to stop her by casting a spell that makes her get hurt. He doesn't want her to fulfill her destiny and will do whatever it takes to keep her from being a threat to his power.
A new emerging criminal who has a grudge against technology and those who use it to catch criminals. Garcia, being the tech genius, would be a prime target for them. They could plan an elaborate scheme to hurt her and disrupt the BAU's work.
It could be another character who is jealous of Lucy's new powers. Maybe a classmate or a rival in her community who wants those powers for themselves and will do anything to take them from Lucy.
Maybe the main antagonist is an old enemy of Robin's who becomes jealous of his new powers. This enemy then devises a plan to steal Robin's powers or at least neutralize them so that he can regain his former status as the top threat. He could be a powerful martial artist or a criminal mastermind with a large network of henchmen.
It could be a rogue angel. There are always some angels in the Supernatural universe who oppose Castiel's ideas or actions, and they might see stabbing him as a way to get rid of him or send a message.