Infection
Rather than being killed by Doomsday, Clark is badly wounded, and infected with kryptonite that has been corrupted via Doomsday's blood. In the aftermath of the fight, with nobody realising the extent of the damage, Clark and Bruce attempt to build something like a working friendship, with Bruce shrugging off the alterations in Clark's behaviour as post-traumatic reaction from having been nearly killed, until Clark, who has been giving in to urges to take what he really wants regardless of the cost to other people, decides to take something he's been wanting since the fight: Batman.
See author notes at the beginning of each chapter for additional content notes. Update schedule will be every second week. The character death tag is for referenced, past character death, rather than character death in-story.