Edit: just learned its an already established theory -w- Theory: Johnny Silverhand and Morgan Blackhand had their minds mixed.

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At the end of Transmission in Cyberpunk 2077, Johnny and V talk. This conversation resonates with me. Whenever I see Johnny, I think of that conversation and what it was about. It's about identity. In particular, the identity of engrams, and Arasaka's ability to take them away. But there's also another thing Arasaka can do: they can mend your mind with another's. Some time later, I looked into the lore of cyberpunk and discovered that Morgan Blackhand took part in the Arasaka raids. Not only did he take part in them, but he also planted the bomb and fought Adam Smasher on the roof of the tower, disappearing shortly after. Then I replayed 2077 and came to a realization: Johnny has memories of things he never did. Now, it's not out of the ordinary for Johnny to have weird bastardized memories of certain events, like him believing Samurai disbanded right before the Arasaka raid when really, they broke up several years before, that's just him phasing out boring parts of his memories and replacing them with his favorite parts. But, may I remind you, Johnny never nuked Arasaka nor did he ever fight Smasher on the roof of the Arasaka Tower, Blackhand did those. Johnny wasn't even there when those events occurred, the two were in entirely separate squads that went to separate destinations and Johnny got his ass kicked far before the two squads regrouped. So he never should've known those two events occurred. It's also important to note that, in the Cyberpunk Red story, Black Dog, it is revealed that Silverhand's body was left in the towers and not carted away like we see in 2077.

I could say more to backup my theory, but I'm getting bored, so let's jump to some conclusions:
Johnny Silverhand and Morgan Blackhand were both in separate squads of the assault on Arasaka Tower. That was the last time they saw eachother. Silverhand was a part of a squad that broke into the Soulkiller labs, after releasing alt, he was intercepted by Adam Smasher, who used the nearby equipment to torture and kill Johnny. Johnny's fate remains unknown however, his squad assumes he is dead as they see him get beaten into a pulp. Meanwhile, Blackhand plants the bomb and is able to make it to the roof but remains to fight Smasher and subsequently loses (but not as much as Johnny), so he is carted out of the tower and taken to a secret Arasaka bunker in the badlands to be a test subject for Soulkiller. His body is discarded and promptly never seen again. Between 2023 and 2077, Johnny and Blackhand are experimented on by Arasaka, these experiments include temporarily erasing their senses of self and combining the two engrams. It's the neural equivalent of tossing a salad, picking out the croutons, then mixing them back in, retossing, and picking them out. Small portions of their memories and personalities are mixed together. Mix this in with the passage of time and you have bastardized forms of each merc, entirely unreliable representations of their former selves. This explains why Johnny acts differently in 2077 and why he knows about the experiments forced on soulkiller victims.

What does this mean? Well, two things. The one everybody knows is that the Johnny in 2077 is not a true representation of Johnny and all of the flashback sequences are unreliable. And the second is that Morgan Blackhand may still be alive, but not in the way everyone thinks. Maybe, if I'm correct, this means Blackhand will come up in the sequel and we get to hang out with somebody far less insufferable.
 
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That is a very interesting theory! And I feel it's grounded right at the beginning, as no, Johnny would not have those memories or experiences.

I also think it follows suit with what's happening to V over the course of the story. Their mind is merging with Johnny's, and they're beginning to affect one another -- change one another's views. (Or, at least V seems to affect Johnny in some key areas. All depends on how stubborn the player is in their ways.) I think you're definitely on to something about the way engram tech was made and what it means.
 
I like your theory. It may or may not be right, but it makes more sense than any version of the "official" story in the game.

The whole thing about the chip overwriting V doesn't even make any sense in the context of the way the story evolves. It's clear that the personality construct on the chip is merging with V, not overwriting V. V is taking on aspects of the construct, and the construct is taking on aspects of V. So, your theory fits that aspect.
 
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