Source: Superboy vol. #19 (2013)
Type: Alternate future
1. A villain who is ultimately responsible for everything even though we've never heard of him and he has a lame name (Harvest). I'm having Apocalypse and Mr. Sinister flashbacks.
2. The villain comes from a future in which metahumans are hated and hunted because they caused some kind of disaster/strife. Days of Futures Past-type stuff, except set in the 30th century, which is way too close to the Legion timeline to make any sense.
3. In his non-zombie form, Harvest has a scar on his eye. Of course. Cable would be proud to call him a cousin.
4. In FACT, there's a lot of Cable/X-Man/Rachel Summers in here, with Harvest grooming the son of Superman and Lois Lane, or at least clones of him (because we haven't achieved Madelyne Prior levels of convolution yet) to be his champion through which metas are destroyed at the root. Potential scions of present-day heroes were all the rage in the X-books, as you know.
5. Lets make it a little grim too, with the original Jon Lane Kent falling dead before the age of four from a great height due to genetic incompatibility. [SUPERMAN/WONDER WOMAN AGENDA PROPAGANDED!] And he looked like such a happy baby, too.
6. The Jon Kent clones last longer and longer under Harvest's creepy tutelage, but they inevitably die because of their paltry Lois Lane genes. You're not an X-Man unless you died a bunch of times.
7. Everything Lobdell established before that doesn't fit in with this story immediately retconned.
So Superboy is now one of these clones made from Superman/Lois DNA and I guess maybe a sleeper agent for Harvest's mad plan to destroy the metahumans like Superman (he's not a metahuman, dumbass) using the scion of the first metahuman (and he wasn't the first, idiot) because it's more poetic that way even though Harvest's own life history has shown that the Jon Kent genome isn't viable. And don't get me started on how Harvest stopped raiding baby Jon's corpse for DNA and went to his parents instead... somehow making a Jon Kent look-alike every time. BECAUSE THAT'S HOW DNA WORKS!