Arguably the subject of the film is the ruinous effect of the obsession graysmith et al decelop with identifying the zodiac killer -- and the maddening impossibility of resolving the mystery.
Yes very true, they make out that it sucked in both Avery and Graysmith and drove them to the point of madness and beyond, and had a similar effect on Toschi until he managed to step back from the void... but I'm not sure that I found the portrayal of this that convincing, one minute they're going "Hmmm, this is intriguing" and next scene they're living in a cellar surrounded by boxes piled high filled with Zodiac clues and the walls covered in insane diagrams seemingly drawn by a mad professor and cross-referenced with cobwebs of pinned threads that look those experiments when they said "what happens when you give a spider crack cocaine?"
Of course they heavily put their thumb on the scale by making it seem obvious that Arthur Leigh Allen IS the murderer, but there are elements of doubt sewn in like the handwriting thing, the creepy ass basement belonging to that creepy ass man etc.
Surely that creepy basement scene was totally made up though, I can't believe that that happened, certainly not as it dramatised in the film. There is a bit towards the end where you have that and various almost jump scares which occur at Graysmith's house and it combines to give an impression that the Zodiac was somehow hunting him in return. I took that to be either a) a totally spurious bit of melodrama chucked in so as to stop the final act dragging so much or b) more charitably it was a way of showing how paranoid Graysmith had become, to the extent that he believed that the Zodiac was hunting him and, to give us some insight into how he felt, they give us events as he may have seen them in his paranoid fantasies rather than as they really were.
A more general question here, does, say, Andrerson's family have any way to take action against someone making a film and strongly implying "Your brother/father/son/whatever is a notorious serial killer" even though there was no really solid evidence to say that this was the case? Cos I have to say, if that were me, I'd be a little peeved about it. Especially as it was such a big film made by Fincher and with a stellar cast - now, you're telling me that Graysmith's book is mainly discredited and its conclusions are not taken too seriously... but how many casual watchers are going to dig into all the alternatives? When you have Fincher's juggernaut with Robert Downey Jr and so on vs on the other hand an actual book written on paper by someone who (as far as I know) isn't even a really handsome superstar then the former has far greater reach, regardless of how well the arguments stack up were one to go and research them independently.