The following article contains spoilers for Dark Crisis #3, on sale now from DC Comics.
Pariah may seem to be the central antagonist of the series, but Dark Crisis #3 (by Joshua Williamson, Daniel Sampere, Daniel Henriques, Danny Miki, Alejandro Sanchez, and Tom Napolitano) casts some doubt on his ability to be the endgame antagonist. Hal Jordan questions his ability to master the Great Darkness, and suggests that the opposite may be true -- the Great Darkness might be controlling him.
Pariah rejected this immediately, but it isn't too far outside the realm of possibility. There is still much to learn about the Great Darkness and the abilities it has demonstrated indicate that Hal's theory may be a fact instead. If so, then Pariah has made the same mistake that destroyed his world in the first place -- he meddled with forces he did not fully comprehend.
When Pariah first debuted in Crisis on Infinite Earths #1 (by Marv Wolfman, George Perez), he was originally a scientist named Kell Mossa. As one of the premier scientists of his reality, Kell wanted to witness the beginning of the universe. His experiments, however, resulted in the Anti-Monitor becoming aware of his universe, and then promptly destroying it. Kell was spared, but this began his long existence watching universes fall.
Ultimately, Pariah blames himself for what happened to his reality because he meddled with powers beyond his comprehension. While he's trying to fix his mistake, he's going about it the wrong way. He has enlisted the help of a power that predates the multiverse and would likely want to destroy it. Rather than be wary of such power, Pariah has embraced it, believing it is the key to rebuilding what was lost. In retrospect, it seems foolish to believe that a power whose only real use is to pervert or destroy life could in any way be utilized to recreate it.
When Hal made contact with the sphere containing John Stewart. He described it as a weapon, something the Great Darkness used separately from Pariah's intended goals. This implies that the Great Darkness is and probably always was in control, meaning Pariah matters very little in the grand scheme of things. If that proves to be true, then Pariah is merely just a pawn and nothing more than a mere assistant.
Another fact supporting Hal's theory is everything the Great Darkness has accomplished so far. It has been known to manipulate great powers that, on their own, are threats to whole universes. More than that, it has outright mind control powers -- look at what it did to Deathstroke or how it trapped the Justice League in their own minds, making them believe that their delusions are reality.
If it can do all that, then manipulating the mind of a mortal like Pariah is child's play. It's probably feeding his ego, restoring the arrogant scientist who believed he could toy with the great powers of existence to satisfy his own desires. In reality, though, Pariah is a toy, and one the Great Darkness will easily discard when his purpose is fulfilled.