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).
Doofenshmirtz could be the antagonist. He might create a contraption that directly or indirectly causes Phineas to get mad. For example, his -inator could accidentally zap away all of Phineas's blueprints for his latest project. Phineas would be understandably angry and would then see Doofenshmirtz as the source of his frustration.
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.
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.
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.
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.
Maybe the little sister gets lost in the backyard which has been magically transformed by one of their inventions into a huge, mysterious maze. Phineas and Ferb then have to use their wits and knowledge of the backyard to find her. It could show their protective side towards their little sister.
Well, it could be about how Phineas tries his best to take care of Ferb. Maybe he builds some crazy contraption to make Ferb feel better, like a super - advanced bed that can do all sorts of things to ease Ferb's illness.
Well, perhaps in the fanfiction, Phineas gets mad because Ferb accidentally ruins one of their big inventions. Maybe they were building a huge roller coaster and Ferb made a miscalculation that made the whole thing collapse. Phineas, who is usually calm and positive, gets really frustrated and yells at Ferb for the first time.
It could be a new neighbor who is jealous of the little sister's relationship with her brothers. This neighbor might try to drive a wedge between them by spreading rumors or causing trouble. For instance, they could tell the brothers that the little sister doesn't really care about them and is just using them for her own gain.