Taken from “Who is Father Flynn” from Bobtherandomguy′s Phineas and Ferb Wiki Blog, slightly modified.
In episode one we are introduced to the Flynn-Fletcher Family (aside from patriarch Lawrence who doesn’t appear until Candace Loses Her Head). Almost right away we are told that Ferb is in fact the Step-Brother of Phineas and Candace which means of course that Lawrence is their step-father. This leads to an interesting question, who is their biological father?
Of note, I will use the term “Father Flynn” because I can’t really think of anything else to call him, evidence suggests Flynn is afterall Linda’s maiden name.
Shortly after the series premiere Heinz Doofenshmirtz was hypothesized to be the father of Phineas and Candace due to his similarities to Phineas (i.e Mechanical inclination) and Candace (i.e He’s insane). Given the fact that the only ex-wife he is shown to have is Charlene, and they have a daughter slightly older then Candace, that seems unlikely however, plus Candace has met Dr. D several times with no apparent recognition. The final nail in the coffin however was that Heinz and Linda had one date back in the ’80’s which would proceed the conception of either Flynn child by quite a few years.
Another proposed father has been mentioned as being Mayor Roger Doofenshmirtz, he does after all possess the same genetics as Heinz,and given Phineas’ natural charisma it does sort of make sense that he would be the offspring of a politician, but once again given adult Candace’s inability to know who the heck Doofenshmirtz is nor even suggest she knew the name prior to that event, it seems likely that Roger did not have a very long political life after present day.
When I wrote fanfiction back in the day I had Lawrence recall that when he first met Linda she was dating her agent, who I listed as the father of Phineas and Candace, then dumped her once she became washed up. However the more I think the more I realize the answer has been around the entire time, obvious to anyone with a different thought process.
While not Doofenshmirtz the father is in fact a member of the main cast. By this point one must be scratching their head in confusion, Father Flynn has in fact been around since day one, Father Flynn is in fact Perry the Platypus.
Didn’t see that one coming did ya, seriously did you? As you may know the average platypus lifespan is not remotely close to that of a human, certainly not in a manner that Perry would have been alive when Phineas was a toddler and also when Candace is 35. This is my thought years before the series the O.W.C.A possibly under different leadership employed Agent P, while on a spy mission Perry was critically injured and had his soul of sorts, implanted into a platypus which the O.W.C.A made sure was delivered to the Flynn Family. To cover their tracks they made sure to employ other animals so no one would become suspicious of why a platypus is amongst a group of human agents.
Perry knows his life as a person is over, and he is happy his wife found love, but he does want to remain a presence in the lives of his children. Notice that he does his best to remain in Candace’s life despite her apparent disdain for him. She was his first born and thus means a lot to him. Due to this he makes sure she knows who her friends are which came into play in Phineas and Ferb Get Busted when he was able to properly characterize both Best Friend Stacy and Boyfriend Jeremy. What about Phineas however, his second child, he’s shown a multitude of times that he cares for Phineas just as much and Phineas has always cared for Perry as a friend, and confident, but it appears he isn’t as interested in his friends since only Baljeet appeared in the episode in question and proceeded to become a strange Puppetmaster controlled by the talking Zebra.
Ah yes the Talking Zebra, Perry knows about him, which can be clarified by the fact that Perry was around during Candace’s hallucinations but could also be explained that Perry as a human was also subject to hallucinations granted to him by the strange Talking Zebra, perhaps the nature of the name “Kevin” is in fact Perry’s human name. Once Perry’s human lifespan could no longer be detected the Animal Spirit went to his next of kin.
Is any of this true, probably not, Dan and Swampy have indicated that the missing parents will never come into play, nor do I think it’s necessary to do so, but ask yourself, the next time you watch an episode, are these the mannerisms of a simple family pet or perhaps a missing father looking out for his children and doing whatever possible to make sure their lives are good. Thank you and have a nice day.