Obviously, there are some reactions that go somewhere along the lines of “What the hell....? What do you mean we shouldn't trust anyone? Who's the main character?”
Christopher Reich once noted that, in a thriller, the reader should always be prepared for anyone to “get it in the neck” at any possible moment, from any possible angle—including behind you.
I started writing in 1998, before there was a television show called 24, where the only one you trust is Jack Bauer. Back then, there was an author named Jeffery Deaver, whose writing style led you to trust everyone... and then stabs you in the back so firmly, the knife blade jams there. Sometimes the killer that Deaver shows you isn't the killer you have to be wary of; usually the shadowy looking figure who lurks in the background and mysteriously disappears turns out to be something different from what you expect (a victim, a cop, an ally that no one knew they had).
It's actually a tradition that goes back to murder mysteries. Agatha Christie has had as murderer: the detective, the narrator, the sidekick, a corpse, and everyone; in “And Then There Were None,” I don't think was really was a main character. There are “police procedurals” where the murderer is someone who was never introduced in the novel, and the last page is filing a warrant for his arrest.
I didn't intend to go to either extreme when I first started—and I don't think the "trust no one" paranoia lasts TOO long. Obviously, there will be people readers can trust during the book... eventually. By page 50 or so, every reader will probably make a decision on who to focus on as “the hero(ine).” And every reader will decide when and who in the story they think is the hero.
It's easy to look at Papal Security Commander Giovanni Figlia and decide that he's a great lead: he's got a wife, two children, a long, established career. And then to look at the “security consultant” Sean Ryan and decide that this guy's nuts: a mercenary who talks about the people he kills with no sign of remorse, puts body counts on his resume, and seems to like what he does far too much. What one does with a Pope that's to the right of Attila the Hun probably depends on one's political leanings.
Funny enough, when I started writing the novel, I simply wanted it clear that trusting someone implicitly was not a good idea. The more characters who slipped their way into the book, the more paranoid it started to seem. Writing Sean Ryan from the point of view of someone who knew nothing about him made him look like a future mass murderer. Seeing a priest with SEAL-level training seems sinister when the reader doesn't know where he got it from. The more they showed to the reader, the more each of them looked like they could be great suspect material.
In the first draft, the whole book started to spiral out of control due to that.
Yes, you read that right, my characters nearly took the book away from me.
There are some authors who have described writing as either schizophrenia or multiple personality disorder. If an author does the job well, the characters you read should feel real to you. In some cases, that's because the author has so well fleshed out the character, the character is alive, and can often make moves that surprise the author. Author Dorothy Lee Sayers wrote an entire book on the subject, using insight as a writer to look at creating worlds from the viewpoint of God—if you ever thought that writers were megalomaniacs, well...in their own little worlds, they are god.
I can only hope that any actual deity finds life far less frustrating than trying to tame characters.
In the original draft, when it was one book and not a trilogy, I had started with a plan of: dead body → conspiracy → stopping conspirators. Simple, straightforward, and very basic.
Enter characters who don't know their place.
My villain had a very well thought out plan. In fact, it was so well thought out, nearly everything the protagonists did only served as speed bumps. Unlike some villains I had used in previous manuscripts, this guy would simply not be a good little psychopath and stay down. I did everything but drop a house on this guy—and in one manuscript, I imploded a building with him in it—but he kept finding ways around it. I considered having someone kill him up close and personal, but every fight I came up with ended in a draw.
So, I let the story play out so I could see what it took to stop this guy.... 200,000 words later, I found out.
The story became: dead body → conspiracy → stopping conspirators' gunmen → fallout → conspiracy contingency plan A → stop that plan → fallout → contingency plan continues with slight modification → help, we're going to die → let's go down fighting → fallout.
So, because of one highly obnoxious character, instead of having a simple novel that was completely contained in Rome, A Pius Man becomes a world-spanning trilogy that all starts because one man found something he shouldn't have, and ends with a recreation of Thermopylae, with claymore mines..
The next time you see a line noting the paranoia in the book, you can at least understand where it comes from. It comes from the same place as an antagonist who just won't die no matter how hard I try to ram a stake through his heart. It comes from fairly strong characters who are, in some cases, slightly more crazy than the author.