PTSD.
Clark has Post-Traumatic Stress Disorder.
And it's not going get better by itself.
He needs to talk to a qualified therapist and get some help. That would require, of course, that the therapist be given his full background - New Krypton, the revolution, what Clark did, what happened to him, and that he is (or was) Superman. And I'm a little surprised that neither Lois nor either of his parents has suggested it. These false steps, like the one closing this chapter, aren't going to solve Clark's root problem.
You haven't been explicit enough yet for us to know if Clark and Zara were intimate. I suspect not, simply because each has hopes for another lover, but they might have been forced into it by societal pressures. That would contribute to Clark's guilt and put another layer of separation between him and Lois. Even if they never had sex, their marriage is a problem for both Clark and Lois, whether either wants to admit it or not. That means that he and Lois have some issues to hash out that are separate from Clark's PTSD.
Good story. Really. I like it. It's heartrending on multiple levels, and there's Kallie in the middle, the most innocent and most vulnerable of them all. It's guaranteed to tug on our heartstrings. Good work. Keep it up!
