You know how, in some time-travel stories, someone will create a stable time loop in which Event One causes Event Two, which causes Event One? That's allowable, by the laws of physics (given that time travel can happen), despite the spooky way that information pops out of nowhere.

It'd be a lot like that.
1. Your agent returns from a mission.
2. He writes a mission report to turn in to the Flowers.
3. Because he's an Author, the mission report causes the mission to occur the way that it did.

Your agent would probably be quite unaware of the process. It could actually be what happens for many World One self-insert agents who write their own mission reports.

...that there are certain departments in the organization that would probably not take kindly to an agent messing with the organization by writing fiction about the organization.

They may or may not exist. They may or not have a Wiki page.

Oh...here it is: the DIO.

We always try to answer questions, but no one can do so within two minutes of you posting the first time. ;)

And to be honest, I'm not sure. There are definitely agents who once wrote fanfic, and agents who are aware that they themselves are being written, but I don't think any agent would take the risk of messing with the already-fragile fabric of reality in HQ. Besides, if it worked, they would essentially have the power to write whatever they wanted to happen happening - that being anything from a payrise to tyrannical rule over the Flowers - and if not, they'd likely be caught by the fellow agents they're writing about and possibly end up in Medical as a result; so says the Laws of Irony and Rule of Funny. I can't see how the former would work out without toeing the line we've tried hard to draw about keeping agents from being to speshul. The latter, on the other hand, could be funny.

But as it seems you're talking about a character who once wrote PPC fics and then joins the PPC... Hmm, maybe. I'm sure some of the agents around this character would be wary, maybe even blame her (him?) for the daily suffering of their work, but it's still rather tricky.

Personally, I wouldn't do it, but I won't say outright that you can. What I will say is that - as you are, self-admittedly, a newbie - you should probably put this idea to the side for now and start by writing more normal agents. If you finish three or four missions like that and still feel it would be a good idea (and, of course, if the other PGs and oldbies on the board don't ask you not to), then you can consider writing in your new, former-PPC-fic-writer agent and see if it works. But please don't ask Permission with this character; it's too soon, and too tricky an issue.

I'm not sure (and I have no authority on this matter) but the PPC guys can open portals to the Real World, and PPC writers exist in the real world, but that would create a new layer in the writer-to-story hierarchy...