Most likely Dr. Doofenshmirtz. He always wants to be on top and if Phineas and Ferb get powers, he'll do anything to take them for himself. He might create some really wacky and dangerous inventions to try and steal their powers.
It could be a new character, maybe an evil scientist from another dimension who is jealous of Phineas and Ferb's powers. This new antagonist would try to take their powers away and use them to take over both their world and his own. But Dr. Doofenshmirtz might also team up with this new villain at some point, thinking he can double - cross him later and get all the powers for himself.
Well, in addition to Doofenshmirtz, it could be some power - hungry government agents. They see Phineas and Ferb as a threat because of their newfound powers. So they try to capture them and study their powers for their own military or scientific gain. These agents would be using all kinds of high - tech equipment to track them down and try to take away their powers, which would make them a major obstacle for Phineas and Ferb.
Well, they might use their powers to build even more amazing things in the backyard. Like they could create a floating city or a time - traveling machine that actually works. And then they'd have to deal with Doofenshmirtz trying to steal their powers for his own evil plans.
Candace could be a main character. Since Ferb is sick, she might be in a bit of a dilemma. On one hand, she still has her urge to bust Phineas if he does something out of the ordinary while taking care of Ferb. But on the other hand, she also cares about her brother and might be more lenient or even helpful.
The parents, Linda and Lawrence, are also important characters in this type of fanfiction. Their reactions to finding out about Phineas and Ferb's activities can vary greatly. Some fanfictions might show them being really angry at first but then realizing that their sons' creativity should be encouraged rather than punished. And of course, their friends like Isabella, Baljeet, and Buford can play important roles too, either by helping the boys or having their own unique reactions to the situation.
Definitely Doofenshmirtz. He could mess with one of Phineas and Ferb's inventions in a way that really ticks Phineas off. Like he might use one of his -inator devices to turn their amazing flying machine into a pile of junk. Phineas would be furious and would then set out to fix it and get revenge on Doofenshmirtz.
Obviously, Phineas would be a main character as he is the one getting dysentery. Ferb would also be very involved as his brother. He would be there to support Phineas and probably try to come up with solutions to make him feel better. Perry the Platypus might also play an important role. Even though he has his secret agent duties, he could still keep an eye on Phineas from a distance and make sure he is safe.
One interesting plotline could be how Phineas and Ferb deal with the aftermath of getting busted. Maybe they have to find a way to convince their parents that their wild inventions were actually for a good cause. Another could be that their friends rally around them to help prove their innocence.
It could be some new evil organization that combines the worst elements of both the Phineas and Ferb world and the Star Wars universe. For example, a group of evil scientists from Phineas and Ferb's world who have teamed up with the Empire's remnants. They could be planning to create a weapon that would destroy all the fun and creativity in both universes.
It could be an evil wizard who wants to capture the phoenix for its powerful magic. The wizard might be jealous of the phoenix's ability to be reborn from its ashes and wants to harness that power for his own dark deeds.
A mischievous fairy who lives in their backyard could be an antagonist. She might be jealous of the attention the kids get and start causing trouble for the little sister. Like making her toys disappear or creating illusions to scare her. This would force the little sister to be brave and find ways to outwit the fairy with the help of her brothers (even if they don't initially believe her about the fairy).
Well, Phineas and Ferb are the central characters. They are brothers with very creative minds. In the 'Scary Story', they are likely to be the ones driving the plot forward, whether they are exploring a spooky place or facing some kind of mystery. Their sister Candace might also be involved. She often tries to bust her brothers' activities, and in a scary story setting, she could add some comical relief or even be part of the overall spooky adventure.