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.
One possible plot could be that Phineas and Ferb build a super - advanced lightsaber - like device in their backyard. Meanwhile, the Star Wars characters mistake it for a new Sith weapon. Then, Phineas and Ferb get caught up in the Star Wars universe and have to use their creative skills to help the Jedi defeat the Sith.
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 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.
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.
A really cool plot could be that Ferb discovers he has some latent Force - like abilities. Phineas then decides to build a device to enhance these abilities. Meanwhile, in the Star Wars universe, there's a new threat emerging that only their combined skills and knowledge can defeat. They have to travel across different planets, meet various characters, and use their unique brand of problem - solving. Along the way, they introduce some of their friends from their own world to the Star Wars characters, creating some really interesting cultural exchanges and comical situations.
One idea could be that Phineas and Ferb build a super - advanced lightsaber - making machine. They use their usual creativity and some 'Doo - hickey' they invented to create lightsabers with unique features like changing colors on command or having the ability to transform into other tools. Ferb could be the one who focuses on the technical aspects while Phineas comes up with the wild designs.
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.
I think Darth Vader and Dr. Doofenshmirtz would make an interesting crossover. Darth Vader's dark and menacing presence combined with Dr. Doofenshmirtz's comical evil - scientist shtick could lead to some really funny and unexpected interactions. Maybe Dr. Doofenshmirtz tries to steal Vader's lightsaber for one of his 'evil -inator' plans, and Vader is just completely confused by this strange little man.