Some thoughts you may or may not agree with. They're there just for the sake of discussing them.
- Alt
This is the grandmother of AIs. Created in 2013, she/it would be 64 year old by 2077. In the Net, that means 2 or 3 eternities. So the change and the supposed loss of humanity. Since Alt is distributed throught the network, it can also be argued that her humanity is in storage somewhere and it/she can access it as it/she sees fit. After Rache's pranks and the destruction of the NET, neither Netwatch or the corps have the power to restrain, stop or kill Alt, and some other AIs. In the game, Alt is a Deus Ex Machina (literally). Her goal is however shady and, as I understand it, stupid. What is it/she to do with engrams / personalities ? What knowledge these personae possess Alt may want ? There's such a hole here.
- Soul
This is a religious word. There is no soul. There is a mind, with a bunch of memories and trends and feelings. But a soul ? Nope, not in Cyberpunk.
This is a game where human can be sum up to a cortex and a spine and put into a full cyborg and you're introducing a soul ? No kidding ? This also conveys the belief of an afterlife for the immortal soul, which is at hand with technology, but that what is offered by technology is not the real thing.
Cyberpunk is about trans humanism, about a way to escape the flesh and its limitations. But I see nothing in the endings about it. On the contrary : no flesh no life (V and Johnny die without a body since they merge with Alt).
- The DNA rewriting and the radiation overdose
I believe that they are simply narrative tricks to set up the 6 month and bye-bye thing. That's lazy of the writers and they do not relate one to the other.
- Cyberpunk is dark, then the endings should be dark
Well, I got another syllogism for you : we all die in the end, so why bother living ?
Shoot...