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.
Another option is a shadowy figure from the mythical underworld. This figure is envious of the phoenix's life - giving and purifying presence in the world. He tries to corrupt the phoenix or steal its essence to spread darkness. Phineas and Ferb then have to face this menacing being and protect the phoenix with their wits and courage.
Well, the plot could involve the phoenix taking Phineas and Ferb on a journey through different mythical realms. They visit places like the land of flying islands or the underwater kingdom of mermaids. During this journey, they face various challenges that require both their scientific knowledge and the phoenix's magic to overcome. And of course, they have a lot of fun adventures and make new friends along the way.
Well, it could be that Phineas and Ferb accidentally stumble into the Matrix world while working on one of their crazy inventions. Maybe they think it's just another wacky dimension they've discovered. They might start trying to build something to get out, using their usual creative skills and the strange technology they find in the Matrix.
In a 'Phineas and Ferb meet Zak Storm' fanfiction, it could start with Zak Storm's ship getting caught in a strange storm that sends them to the world of Phineas and Ferb. The two groups meet and are initially confused. But then they discover that they can learn a lot from each other. Phineas and Ferb show Zak Storm and his crew how to have fun in their own unique way, like building a giant waterslide in the middle of town. Meanwhile, Zak Storm tells them about his seafaring adventures and the magic that exists in his world. Eventually, they have to work together to get Zak Storm's ship back to his world. Ferb might use his skills to repair any damage to the ship, and Phineas could come up with a way to create a portal to send them back.
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.
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).
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.
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.
It could be Dr. Doofenshmirtz. Since he's always causing trouble in the Phineas and Ferb world, in the crossover, he might see Mom as an obstacle to his latest evil plan. Maybe he's trying to take over the neighborhood where Mom lives, and Phineas, Ferb and Mom have to stop him.