Even Candace could be seen as the antagonist in a sense. If she constantly tries to bust Phineas's projects when he's already in a bad mood due to other reasons, her actions could be the final straw that makes Phineas really angry. She doesn't mean to be a 'villain' but her actions in the context of Phineas's already frayed nerves could make her seem like the antagonist for a while in the fanfiction.
It could be another kid in the neighborhood. Maybe this kid is jealous of Phineas's popularity and his ability to create amazing things. So, he tries to sabotage Phineas's projects. He might spread false rumors about Phineas or physically damage his creations, which would make Phineas really mad and see this kid as the antagonist in the story.
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.
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.
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.
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.
Another possibility is that in the fanfiction, Phin gets mad when someone from their school, like Buford, teases Ferb too much. Phin is really protective of Ferb. So when Buford makes fun of Ferb's accent or his quiet nature, Phin could get really angry and decide to teach Buford a lesson.
Maybe Phin gets mad because Ferb keeps taking over their projects without much consultation. Ferb is often very methodical and might start changing things in their grand plans, which makes Phin frustrated.
It could be Perry the Platypus, in a really unexpected turn. Maybe Perry has to keep some secrets from Phineas for his spy work, and one day those secrets are revealed in a way that makes Phin feel betrayed. This would definitely make him mad.
Isabella might also be involved. She has a crush on Phin. So when he gets mad, she could come over and offer her support. Maybe she'll bring some of her Fireside Girls cookies to cheer him up.
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.
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.