Supernatural has its own page for who the main villain of each season is. I don't know if this wiki's going to get one but basically I'll make a list and see if we can agree on it.
Also listing secondary antagonists, but forgive me if I don't remember a whole lot from Seasons 3 onward
Main - Victor Drazen. At first it was Gaines, but he was working for Andre, and it's later revealed Victor was somehow in contact with Andre the whole time he was in prison and thus he seems to be the mastermind behind the day's events. Ultimately the highest up the chain of command here.
Secondary - Andre Drazen, Ira Gaines, and Nina Myers. Also Carl Webb and Sherry Palmer for David Palmer's subplot.
Main - Peter Kingsley, who orchestrated the whole …
Wikipedia acts like it is, and Max's article lists his death there.
Though, I'm a bit iffy about this because Wayne said that David Palmer "arrested the man behind the attempt on his life", which is Max, and Trepkos didn't really know anything about that. Which seems to contradict his being shot by Jack.
So, is the game actually canon to the show?
It never just occurred to me until now, but I just got to Gaines's death episode where Gaines told Kevin that if you fail the Drazens or try to leave them, they WILL find you and kill you. That's why he was so confident Jack could never protect him despite the offer.
Now, Jonathan Matijevich was unable to kill David Palmer, the job he was specifically hired for. Yes, this was due to Jack's interference by grabbing Alan Hayes's gun, but he disappeared after that and Andre sent his brother Alexis to kill Palmer in his place, why?
It is specified he escapes, and that CTU agents were looking for him, working out that he was involved due to deducing the real Martin Belkin's fate. It is also specified that he never got back to Gaines after the ass…
(Spoilers if you haven't seen the end of Season 1, but I'm sure most people here have)
Did Gaines know whose side Nina was really on? Had the writers decided it at the time? If not, they did such a great job at hiding Nina's true allegiance throughout the first 20 or so episodes, even using her as a "red herring" at the beginning.
Now you may have heard the term "FanonDiscontinuity" on TV Tropes. It means you put a certain sequel, episode, arc, etc. out of your "headcanon", like people do with the Garlic Jr. or Buu Sagas of Dragonball Z, or all the Halloween movies starting from Halloween 4 (3 isn't counted here because it is non-canon). I myself have done the two holiday episodes of Pokemon because they're out of place (besides Snow Way Out was too depressing), and although I haven't done so yet, I sometimes consider doing it for Seasons 7 and 8 of 24.
This was easily my least favorite season. First, Bill Buchanan dies, one of my three favorite characters. But another of the three, David Palmer, dies in Season 5 so that's not too big an issue exclusive to Season 7.