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.
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.
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.
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.
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.
One possible plot could be that someone ruins Phineas's big invention project. Maybe Doofenshmirtz creates a device that accidentally targets Phineas's backyard and destroys all the materials for his amazing new roller coaster. This makes Phineas really mad and he decides to go on a mission to get back at Doofenshmirtz. Ferb tries to calm him down but Phineas is too angry at first. Then they end up working together to not only fix their project but also teach Doofenshmirtz a lesson about being more careful with his inventions.
Perhaps Phineas gets diarrhea right before a big event they were planning, like a huge backyard invention showcase. This causes chaos as they have to delay the event. Meanwhile, Candace, thinking this is a perfect opportunity to get the boys in trouble, tries to call their mom. But Ferb manages to keep her at bay while also taking care of Phineas.
One possible plot could be that Phineas gets dysentery right in the middle of one of his big summer projects. His friends and family then have to figure out how to take care of him while still trying to keep their daily adventures going. Ferb might take on more of the leadership role in their projects while also looking after his brother.