The Real Dad Theory
The Gist of It: DoofenDaddy is Phineas's biological father.
Conversation: This conjecture is mostly based on them sharing a similar head shape, but leads to several other ideas.
Firstly, being the son of a scientist explains why Phineas is so intelligent. It also answers why they appear to have infinite funds, possibly because of a trust fund or similar that Phineas has access to.
Phineas also appears to have little to no care towards any side effect caused from their creations. The giant rollercoaster that goes through town would have caused multiple crashes. For example, they carved Candice's face into Mount Rushmore, they made a time machine and destroyed the timeline, they held a medieval jousting tournament, and they built an escalator to THE MOON. And that's just the first half of season 1. This is possibly a hereditary defect from DoofenDaddy.
Also, it is possible that Perry's mission is solely to prevent the meeting of father and son. If they were to meet, the two geniuses could wreak havoc together, especially because Phineas has a very moldable young mind.
Here is another theory that is almost the same as the previous, but there's more to it:
Phinias is Dr. D's (idk how to spell his name) son, just like Candice and the girl representing dr. D's daughter (i think its Isabella) and they have the same mother, the one representing Phinias's and Ferb's mum. And that's kind of obvious cause both Phinias and dr. D have a triangle head, and Candice and Issabella basically look like the same person. Now, my theory is that Ferb is a son from the guy representing their dad (they both have the same head shape) and that he brought Ferb with him after he got a divorce, and its the same with the mum - she and dr. D get a divorce, she keeps Phinias and Candice, and dr. D gets Issabella. And the only thing bugging me is WHO IS FERBS MUM??!?!? I've looked EVERYWHERE and i can't find ONE person with green hair in that show thats not Ferb..... So the mystery stays unsolved...
The Imagination Theory
The Phineas & Ferb Theory says that the real Candace has lost her mind due to bad things happening in her life.
The theory says that Phineas was her little brother & he was bullied a lot in school because the other kids thought he was too nerdy. One day a bully punched Phineas in the head really hard & it killed him.
That day changed Candace forever
Candace couldn’t deal with Phineas’ death so she built an imaginary world where he was still alive & playing with her step-brother Ferb. Ferb has a disability & can’t talk or do much, but she imagines him and Phineas going on great adventures together.
The real reason why her mother can’t see the things that Phineas & Ferb build is that, well, they simply aren’t there. And the more Candace tries to convince her mother, the more crazy she becomes..
The villain of the show: Dr. Doofenshimrtz is actually Candace’s psychologist whom she’s been seeing twice a week. It started to put a strain on the family to try & pay for all these expensive doctor visits though. In desperation her mother had an idea to write down all the fantastical stories Candace was telling her & try to sell it to Disney as a show, and it worked.
The biggest bit of evidence that goes into this theory is in S2E33: Wizard of Odd, where Candace goes into a parody of the Wizard of Oz with Doof as the Wicked Witch. This means that Candace knows about Doof & his evil intentions, because of which it could be inferred that Candace made Dr. Doofenshimrtz, Perry * their rivalry up.
So that’s The Phineas And Ferb Theory, but is any of it true.
Doofenshimirtz is Unknowingly helping the OWCA
Dr. Heinz Doofenshimrtz is portrayed as the show's main antagonist, But some don't see him as much of a threat. I mean come on he's technically not all that bad. As much as the doctor claims to be "evil" he's more of a disgruntled Mad Scientist, and less of a dangerous criminal. (Which explains why he never gets arrested or goes to jail at the end of the episode).
But the real reason Doofenshimirtz is "getting away" is because the real reason why Perry the Platypus is going to "foil" his schemes, but Perry is actually spying on his "Something-inator", so the OWCA could try and replicate them and work out the flaws so Doofenshmirtz's inventions will actually work.
in the movie, Phineas and Ferb: Across the 2nd Dimension, they have his "Amnesia-inator" in storage which proves one of the theories too. It would also explain why they are watching him vigilantly so Perry can track him down and find him.
So in conclusion Dr. Heinze Doofenshmirtz is not necessarily the evil villain we all thought to believe, he is so undercover that not even he knows what the intentions are. He is technically an unpaid research and development department, so a government agency can steal his work to benefit to them so they can catch the REAL evil villains and criminals on the show who are a real threat to the public.