To be fair, it certainly helps to know the lore of the PnP game.
Coincidentally, numerous shards you find actually explain a bunch of it. It helps to read them. Also, give the CP 2020 sourcebook that is included with the game as bonus content some perusal. It also explains a lot of the backstory here.
From the moment CDPR gave away that Johnny was on a chip stuck in the protagonist's head, I simply KNEW that the story would have something to do with Alt Cunningham, the inventor of SoulKiller. Johnny's love. She died in 2013. Arasaka had kidnapped her from ITS Corporation after she had invented SoulKiller to force her to remake it for them. Then Arasaka stuffed her INTO SoulKiller. Johnny went in to save her, but her body was dead. He didn't know she had been "sucked into the machine" so to speak.
So in 2023, Johnny nukes Arasaka cuz he's pissed at them regarding what they did to Alt. And uses a bunch of anti-corporate rhetoric to justify it to himself (and others?) Unbeknownst to Johnny, Saburo Arasaka had ALSO planted his own nuke in the bowels of the Arasaka building. I forget exactly why off the top of my head, but IIRC it had something to do with all the engrams they had captured using SoulKiller. So Johnny's nuke set off Saburo's nuke, making it all much worse. (Johnny's nuke was 2 kilotons. He just wanted to take out Arasaka. IDR how big Saburo's nuke was)
And this is all simply assumptions and such on my part from prior knowledge. I haven't yet gotten to any parts of the game actually involving Alt. She's only been mentioned once so far in my 60-ish hours of play time. ... Well .... She's also all over advertisements. The blond girl with the gold cyberarm who is kneeling and wearing a fairly skimpy onesie while looking seductively at the camera? Yeah. That's Alt Cunningham. Straight from the Cyberpunk 2020 main sourcebook. There's also a memorial to her in the Columbarium. (there's a few other cool easter eggs there too, as well as memorials to some real-world people)
One of the coolest things about this game is how much lore is actually in there. It's solid. In fact, the newest version of the PnP game, Cyberpunk RED, was created in conjunction with CP 2077 such that Cyberpunk RED is "prequel" to CP 2077. It sits between Cyberpunk 203x and Cyberpunk 2077.
Others have also pointed out how the game's beginning actually DOES make sense as well.
Takemura failed in his duty and feels he must A) Make amends and B) Seek vengeance.
He knows V is the last living witness, and the only person who can help restore even a fraction of his honor, so he keeps him alive.
Dex was a loose thread and had to die. You say, "We should have been given the choice of what to do with Dex." .. um .. Dex shot V in the head and tossed him in the dump and left him for dead. How is V going to have ANY say in what happens to Dex after that, especially after Takemura tracks him down.
Yorinobu wants Takemura out of the picture. Takemura was his dad's man, and Yorinobu has Adam Smasher. Takemura is a threat to him.
There is only one of THIS particular iteration of the relic. It's a "development" version. If you pay attention to the shards you find as well as the advertisements and news broadcasts in the world, you'll see that Arasaka is actually marketing Relic tech to super rich people, to sorta keep their loved ones around. They can either chip it in or perhaps put it on a holo-projector or something and interact with them after they've died. THIS version of the Relic is intended to completely "overwrite" whomever the chip is put into. This would essentially allow physical immortality, ala sleeves and stacks in Altered Carbon. As such, this version is SUPER DUPER important. As to why Johnny is on it? I'm not sure ... yet. I'm guessing the game will explain that eventually.
Here's some important lore on Alt, and thru it you can jump around to learn more of the lore. The story certainly makes more sense with it. And read the shards you find!! Seriously. They're not just "filler" material.
Altiera Cunningham, better known as Alt, was the best netrunner in Night City during the 2000s-2010s. She was described as a beautiful and talented woman; having worked for the ITS Corporation, and being the developer of the infamous Soulkiller program. Cunningham was also the girlfriend of the...
cyberpunk.fandom.com