- Phineas and Ferb has a lot of stories where Perry somehow becomes a human, and oh, it also turns out he and Dr. Doofenshmirtz are both gay. Often Dr. D is the one who transforms him in the first place, though usually for ostensibly different reasons. Ironically, there's an episode where Doof turns himself into a platypus to fight Perry.
- It's common to speculate about the boys' respective missing biological parents. This contains a whole subgenre where Doofenshmirtz turns out to be Phineas's father, with various back stories trying to fit this into canon. This is, of course, greatly helped by the somewhat similar head shapes and the reveal that Doof and Linda actually did go on at least one date when they were younger. However, this specific theory has been jossed by the creators, though this doesn't stop some people from writing about it.
- It is very common practice to make Ferb's biological mother abusive, as an explanation for his quiet and reserved attitude. Conversely, she left Lawrence and Ferb because he was mostly nonverbal.
- It's become somewhat popular to make Phineas and Candace's biological father a Jerkass to some degree; this is mainly so the author can have a scene where the man shows his true colors (often after kidnapping Phineas) and Phineas takes it badly.
- A lot of fanfics put the kids in school. Since the creators have stated that the series will only cover time off from school, there seems to be a general fandom curiosity as to what school is like for the characters.
- A very popular plot in fanfics is aging the characters into high-school, and sometimes further than that into adulthood. Hilarious in Hindsight given that one of the last episodes not only dealt with this very idea, but enlisted a fanartist well-known for working with this concept to make the aged-up characters designs.
- At the end of Phineas and Ferb the Movie: Across the 2nd Dimension Isabella kisses Phineas on the lips just before they're hit with an amnesia ray. This has become a convenient plot device for a lot of ship fic writers. The most common variation is that Phineas or/and Isabella remembers the kiss somehow (very often, the memory returns to them in a dream), and decides to act on it. Another variation is that Phineas gets Carl to stop long enough for him or Isabella to write down a message to themselves.
- Fanfics about everyone's memory getting returned are very common.
- In the movie, during Doofenshmirtz-2s Evil Gloating, he threatens to turn Perry and Phineas into Cyborgs. This mental image stuck around in the fandom, and many What If? fics see the threat fulfilled. Once again, Break the Cutie abounds for Phineas Flynn.
- It is quite common for some fanfics to show characters being related that might not be related in the show (such as Stacy Hirano and the Fireside Girl Ginger, though this one has since become Ascended Fanon).
- One popular topic is the day that Isabella first meets and/or gets her crush on Phineas.
- An increasing trend is to put the Fireside Girls (either individually or as a group) as the main character/s. This is mostly due to the rumors of a Fireside Girls spin-off show.
- The Meap Me in St. Louis story that the creators have no plans to create.
- One of the titular characters gets kidnapped, typically Phineas. The reasons for this vary but include: Kidnapped Scientist, someone trying to blackmail the person not kidnapped, something involving the kidnapped character's missing bio parent, revenge (especially if Thaddeus is involved) and Doof trying to stonewall Perry.
- A Us where human!Perry is a member of the Flynn-Fletcher family, usually related to Lawrence in some fashion, are pretty popular and frequently involve Perry/Doof shipping.
- And then there's the variation of "human!Perry is related to Phineas and Ferb" where Linda and Lawrence are dead and Perry is raising Candice and the boys with Doof's help.
- Crossovers with Milo Murphy's Law were naturally popular from the very first episode of that show, even before the announcement of an actual crossover.
Fandom Specific Plot / Phineas and Ferb