I knew it. "Ghost in the Machine" was just the beginning. Verifying that, in the Bones universe, ghosts are as factually real as the psychic powers used to sense them. I was hoping that episode was just a fluke, a failed attempt at something different. "Shot in the Dark" has confirmed that it was not.
What the hell is going on with this show? This is supposed to be a show about scientists doing science, and Brennan's character being a believer in facts and evidence over faith in anything supernatural was central to this theme. This so-called epiphany goes against the very point of her character. More than that, as pointed out by other posters, it blatantly perpetrates the worst misconceptions about atheists: That not believing is the result of something 'being wrong' with the person; that atheists are cold, emotionless people who live unfulfilled lives devoid of any kind of warmth or happiness; that Brennan's non-belief has somehow limited her in her life, despite the fact that she's one of the most renowned and successful experts in her field, she's in a relationship with the man she loves, has a daughter, and is surrounded by friends of all different perspectives that do nothing but enrich her life experience.
In the end, this episode, like so many before it, but particularly "Ghost in the Machine," was nothing more than sloppy storytelling, lazy writing, and propaganda, plain and simple. And though I'm an atheist, I'm less offended by the (oh-so-common) prejudice against non-believers and more offended by the sheer absence of logical character behavior and progression. I'm all for the "humanization" of Brennan's character. There are already many avenues through which she can experience this, which I've already mentioned, that have nothing to do with believing in the supernatural, which in science, is so irrelevant as to be non-existent.
Get the fricken fairy tales out of this science show