Wow! What an amazing (though very dark) tale. Clark/Kal as the Son of the Luthors is an interesting perspective. I remember a Smallville episode where an alt-Clark was raised by Lionel Luthor and became an evil rogue.
I also like the idea that both Lionel and Lillian were good philantropists and only Lex was always the bad guy... This one shows a really dark version of Lex.
I can understand how and why Clark changed the way he did under Lex' control. I loved the way you showed his change throughout the story.
It was fascinating so see also the change in Lois - from the person who would love to kill her family's murderer to the one who loves the same (though changed) man.
I also liked the way you characterized Bruce Wayne here. I'm not really a Bruce/Batman fan and I regulary don't like hi as a character, but in this one he was in interesting antagonist who becomes a protagonist later, Aan I would say that he also changes during the course of the show. (Wonder if he is or ever was Batman in this universe.)
By the way: Who is Jason? Is this your version of Dick Grayson/Robin? (like I said, don't know much about Batman)
The ending was definitely unexpected. don't saw this coming at all. But, in some way, it was inevitable for this dimension that Clark dies...
I don't know "Assasins Creed" (never heard of that) so I can't say anything about the parallels to that series, but I assume that this isn't necessary to understand the story.
Great (and fascinating) work!