A young hero falls under the shadow of a dark power
That hero is Adam, and the dark power is Cyrus, who in this metaphor is God (and what an anti-God he makes, if we do say so). But the real dark power isn't Cyrus himself so much as the dynamic he creates between Adam and his brother Charles, who becomes the unloved, jealous, vindictive son. In other words, the dark power here is the Cain-Abel curse.
Things are going reasonably well. The threat even seems to have receded.
After Cyrus dies, it looks for a while like Adam and Charles get along reasonably well, but we know that it's not going to last—especially once Cathy comes along. Remember when Charles says in his letter to Adam that he felt like something between them wasn't finished? That's because it's not.
But it comes back again in full force until the hero is imprisoned in a state of living death.
Adam thinks that he can run away from all his baggage with Cyrus and Charles by starting a new life in California/Eden with Cathy/Eve, but then she literally blows that idea to pieces. Adam really is in a state of living death (he says so to Samuel Hamilton) after Cathy leaves.
This continues for a long time. When it seems like the dark power has completely triumphed…
Now we shift over to the twins. For a while it looks like Cal and Aron are doomed to re-enact the same tragedy as Adam and his brother, where one of them will feel compelled to destroy the other as a result of daddy's favoritism. In fact, that's exactly what ends up happening.
… there is miraculous redemption.
But at the last second (and we mean the very last second, as in the last few lines of the book), Cal/Cain is given the choice: He can go on being the fratricidal murderer and feeling sorry for himself, or he can break the cycle and choose not to inherit all of his parents's problems. Choice is good.