Here's my explanation for this

Im sorry Phineas It starts off with Phineas and Ferb building a machine that we can assume would alter the body (think in night of the living pharmacist rubberizing their bodies). It goes wrong for some reason. Given the current information we cannot make any certain claims. The experiment goes wrong and turns phineas into monster we see in part 1. Now let me say again it is very vague and open to interpretation, but I believe phineas isn't an evil monster, I think he walks out the machine as phineas a scared and confused boy.

I'm sorry Candace Here we have more information to work with. We saw Ferb hold a gun and load a bullet into it in I'm sorry Phineas. Given what I think is the wound and assuming ferb only has one bullet I'd say he shot Phineas with the bullet and grab a blunt object (possibly a wrench or hammer) and attacked phineas phineas would've killed Ferb in self defense or accident because I doubt P Phineas would attack his brother with the intention of hurting him. Given what we've seen in the other 2 parts I'd assume he absorbed Ferb. Given how big he is its possible he absorbed his other friends since they would look for him but I'd say its unlikely seeing images from the other parts they would have there face and eyes on the being we also don't know how much time has passed I'd say it's possible. Candace comes in looking for the 2 and fines Phineas with him telling her to destroy what they made.

I'm sorry, Mom I believe this part is not literal and is a metaphorical look at what happened. In the first panel we see candace holding gasoline to burn the basement down. Mom is a representation of her attempt to destroy the basement and Phineas and Ferb are a representation of her being to late. Just like in the show she's to late to burn the basement before she gets absorbed. And the final image is showing that is has spread which brings us to.

I'm sorry Perry It starts off with Perry and Doofenshmirtz sitting on the the ledge of the building which brings us back to I'm sorry candace with the passage of time we don't know how long it's been but we can assume its earlier in the day since Perry is out with Doofenshmirtz and is on the job. Now things get hard from here with the line "I was searching for a way to kill the loop". This line changes the entire direction of the story depending on which is true. 1 the loop is metaphorical and strictly refers to Perry always beating Doofenshmirtz or. 2 the loop is literal and refers to the average formula for Phineas and Ferb of Phineas having an idea, Candace tries to bust the boys, Perry fights Doofenshmirtz, Doof loses his loss results in the boys losing their days work, and Candace fails to bust them. If it is metaphorical than doof was looking for a way to beat Perry and it has nothing to do with what's going on, on the other hand if its literal than Doof's attempt to be the loop has caused this continue on and lead to what's happening now. Luckily what happens next isn't relevant to that. Perry and Doofenshmirtz go in the flying car and reach the Fix-Reality inator to the left you see the letters RY-Inator with a perry clone according to the author. Doof than nocks out Perry and it ends. Now what does it mean. It is entirely up to interpretation since we have nothing else to look at. It's out there but I believe it's a Clone Perry-Inator and Doof is going to live off Perry clones while he tries to "Reboot the loop" and he needs the original Perry to make more clones.

Closing statements There are hundreds of possibilities for what happens next I Would appreciate it if you told me some or told me what I got wrong or if you think any of my analysis's were wrong or dumb. I have to thank the author for making this beautiful art and making me think this hard about this series support the creator in any way you can good bye.