Yeah if you don't hack ARC between the time the top agent is killed and the time of the first Revelation attack, you'll essentially "skip" the storyline. The various story events will occur without your involvement and you can still see them on the news screen, but you can't actually interact with them.
I actually think it's nice that the storyline is optional, because it means that you aren't forced to side with Arunmor if you want to just keep playing indefinitely, nor do you have to worry about that tricky outbreak mission either.
Really though, the breadcrumb trail is laid on pretty thick IMO, at least if you've been following the news. ARC is definitely up to something, and the game certainly encourages exploration and independence. The posthumous email even lights up the ARC mainframe in green on your world map if you needed more of a hint. It's unfortunate that you missed the opportunity unintentionally, though. Sadly I don't know of any savegame editors, so you might just have to start over. Personally I enjoy the earlier stages of the game more than the later ones because you aren't swimming in credits with nothing to buy, so perhaps it's not too much of a loss. Both sides of the story are definitely worth doing, though.
