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.
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.
A really cool plot might involve Candace teaming up with an unexpected character to bust Phineas and Ferb. For example, she could team up with Doofenshmirtz. They both have their own reasons for wanting to stop Phineas and Ferb's projects. But as they work together, they start to see things from a different perspective and might even end up becoming friends with Phineas and Ferb instead.
Candace is obviously a very popular character as the whole concept often revolves around her. She's the one with the mission of busting Phineas and Ferb. Phineas and Ferb themselves are also really popular. Their crazy inventions and carefree attitudes are what drive Candace's need to bust them in the first place.
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.
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.
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.