Dark!Roger is what canon stated him to be in the beginning - the lie Ultra sold. He’s a terrorist (so is canon!Roger, technically), he’s manipulative, he’s dangerous. He cares for Marla but he was honest when he told her he didn’t love her anymore (and a large part of that was her inability and unwillingness to be a paranormal and PRETEND to be a human) - and if that’s what she’s going to do, he’s not going to be a part of her life. To be honest, if Stephen had turned out a paranormal and Luca hadn’t, he’d have been willing to let her keep Luca and take Stephen, he’s a bit of a speciest like that. (However with both parents being paranormals, I HIGHLY doubt Luca is human. We don’t know the breakdown on the genetics but it’s unlikely Luca isn’t a paranormal - Stephen broke out late, after all.) And while he’s the leader John has sold him up to be, he’s no messiah. Basically, Roger is that dark, warped, cunning individual that Jedikiah warned both John and Stephen about. However, he still very closely parallels canon. He loves Jedikiah, he deeply loves his children - and that includes John - he mourned Killian’s death, he strongly believes that paranormals can’t kill and shouldn’t kill, and regrets what they’ve done to John (and the Annex project in general). Dark!Roger is dark, twisted, but not evil - the same as canon!Roger is good but not white in terms of alignment if that makes sense? In many ways, Dark!Roger mirrors canon!Roger. (And as a side note - dark!Roger HAS killed someone once, and he agrees with John - it takes a part of your soul you don’t get back. He won’t do it again, even if he knows it was needed at the time, and Jed’s the only person who knows happened - that event and being institutionalized briefly as a teenager are the events that warped Roger.)
Darker!Roger on the other hand…he’s a monster. He didn’t start out that way (who does?) but he is, and that’s something that Jed has known for a long, long time. But just as in canon, Jed loves Roger and isn’t willing to hurt him - he was even LESS willing as a teenager and too young to really understand what to do. Darker!Roger as I’ve said before, constantly fucks with Jed telepathically, and not in just the (nonconsensual) benign way that dark!Roger messes with Jed. Darker!Roger full scale mindwipes Jed when Jed stumbles onto something that he isn’t supposed to know or gets too out of line. Darker!Roger uses biology against Jed, uses how the body responds to touch and his telepathy to make Jed really dependent on him. To say the least, darker!Roger isn’t capable of love though he fakes it well. Marla in that verse left HIM - it wasn’t Roger moving the family around, though he did spend a year doing that, it was Marla moving them for a while get away from darker!Roger because he fucking scared her. He wasn’t ever violent towards her but she saw more of him with the mask off so to speak than he intended and she took the boys and RAN. She’s careful not to bad-mouth him in front of the boys, but she means it when she says they are better off without him. At this point, he’s a threat to her, because she took his children and they are strangers to him - and Roger really sees people as property. His brother, his sons, etc. He doesn’t wish them harm but he will hurt them to get his way, and God help you if you take something of his away. In that verse, he and Bathory WERE friends, as much as he’s capable of having friends, and for quite a while, Jed was shut out of a lot of Ultra’s power structure. It was really the Arc that caused a rif between the two - darker!Roger used the machine as a weapon, repeatedly, killed paranormals that had been stripped of thier powers, ones TOLD they were going to be released. Partly, because he saw this as a kindness - better death than to live maimed like that, partly to prefect that way of killing, and partly because honestly? He enjoyed it. Bathory wanted to put a biomemetic lock on the Arc so that it could ONLY be used by the two of them together, darker!Roger refused. Both of them spread the rumor of The Refuge and you’ll be hard pressed in that world to find ANY known paranormal that hasn’t been shot up with The Tracer. What only a select few in Ultra know is that Roger can stop time very very well - select and chose who is in the loop and has used that leave paranormals OUT. That is what sealed the rift between them. Because, ultimately, Roger can kill - has killed, repeatedly, uses the threat of being stripped of your powers and then killed as a threat to keep others in line, and Bathory cannot. The war at Ultra is less paranormal vs human and more Bathory vs Roger. Both want to take over, to purge the world of humans, both would be cruel dictators, but neither is willing to yeild to the other. Also, in that world, darker!Roger's death wasn't faked - he's ALWAYS been at Ultra. In that world, when Stephen was taken and his hood pulled off? Roger was sitting across the table from him. He also fully intends to kill Jed when he's done with him, which isn't something Dark!Roger would ever think of doing unless Jed became a threat to him. Also darker!Roger came really really close to killing Morgan and the child, however indirectly - dark!Roger on the other hand, once he’s made it clear to Morgan he will NOT tolerate anyone trying to get more of a hold on Jed than he has, is actually very protective of her especially after she tells him about the pregnancy.