No, I didn't think Zara was pregnant. I thought it meant that by him not going with her to New Krypton, he was losing a
future chance of having children.
I thought it interesting that this came up because I immediately thought of my story 'A New Hero'. Zared, who is Clark's oldest son (and raised by Lois til she died), is also Zara's son. (No, they didn't do the deed. Clark knew nothing about it.)
Sorry it took me so long to read part 4 and post feedback.
So! Tempus is the bad guy.
I noticed the use of the word 'use' wasn't clear in a couple of spots.
And other than for those he didn’t use to fly around the world so much.
I'm not entirely sure what you meant with this one.
....
With this one:
Clark sped up. But with Lois, he couldn’t fly as fast as he used to. They would need a few hours to get to Germany.
It should be... he couldn't fly as fast as he usually did. Used to would give the impression that you meant he just plain couldn't fly as fast as he once did.