I've already responded to the author-wraith concerns in my reply to zdimensia - I've ditched that concept, and instead Falchion retains memories of experiencing the particular fic I'm sporking from the Gary Stu's POV. He would later research the author and realize that he is the current persona of that author.

The canon turning into a monster actually happens in the fic I'm sporking (again, see my reply to zdimensia), because the antagonistic character replacement wants to use her as a weapon and mutates her accordingly. It... doesn't end well for him, I'll give you that much. And while I do plan for the possessed canon to transform before Falchion can exorcise her, he'll remember a couple of small details that will allow him to bring her back down to size without too much trouble. He's rather observant like that. Though he may end up having to rope one of the stronger OC Stand Ins to help him out... new recruits, anyone?

The badfic I plan to tackle for the agents' first mission happens to be of my own creation, unfortunately: "Rise of the Galeforces", a really crazy mega-crossover that primarily takes place in The Incredibles continuum, crossing it over with Portal and later, Jurassic Park. It's in four episodes and available on both Google Drive and DeviantART, but I'm going after the Google Drive version for convenience.

Episode 1: https://docs.google.com/document/d/1J58DHm5dFEndaQq-krzdJJs7iq7AkT7d0zuWAo35Qo
Episode 2: <a href="https://docs.google.com/document/d/1CfQS2gmVZCgrbMaAsR4k3WWZpGbkToOYojFs37ySsY">https://docs.google.com/document/d/1CfQS2gmVZCgrbMaAsR4k3WWZpGbkToOYoj_Fs37ySsY
Episode 3: https://docs.google.com/document/d/1sDmdwFggmwpcnZY1DvZZClv7EjkrIY4Y9hCZDINDahg
Episode 4: https://docs.google.com/document/d/1mEWIdcvDq3wQo0r5M5ekYy4Z5TrVg1B0DqGLJMte03E

As an alternative to the author wraith suggestion, I may play out Falchion's coming to grips with being a persona as follows: He comes to the PPC with a particular set of memories and interests that he doesn't remember having. Then, as the mission plays out, he starts remembering them from the perspective of the Gary Stu self-insert who first appears in Chapter 5. He later goes off to research the fic and the author and realizes that he is the persona of said author, allowing him to remember all the mistakes he made on a personal level when he wrote the fic, and take down the Sue-wraith who begins possessing Violet near the end of Episode 3. (Rose gets rid of the Gary Stu, since Falchion can't bring himself to kill another persona of his.)

I like to think that Falchion has to take on the killer author wraith himself, because I plan for the agents to step in just after the horrifically gruesome death of the villainous character replacement near the end of the last chapter before the epilogue. Rose will have witnessed said death and would be so shell-shocked by it that Falchion would have to take matters into his own talons. He forgets to set up a containment circle, though (and doesn't get the time to remember), and ends up having to fight the wraith on its own terms. It'll still take on the physical form of the monster it turned Vi into, but yeah, Falchion screwing up could also add more drama as he takes that thing down.