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In the 'Chipp'n In' quest we visit Johnny's Grave with Johnny. He seems a bit disappointed that he doesn't even have a marker. Just the words 'No Future' in dried blood on a piece of sheet metal. I assume it covers his remains.
I was thinking that maybe the DEV's could add another side-quest in for that?
Narrative: V get's the storyline mission NOCTURNE OP55N1 where he has to visit Hanako at Embers. V walks toward the door where the two guards are. Before he gets there, Johnny appears and asks him to wait in his own way. The player makes the choice to see what JS wants. He asks you if he can take control again and you say yes. Except this time You meet him at the highest point in the desert mountains that overlook the city.
When you get there, he asks you to take the pill. Johnny takes control of you and drives his Porsche 930 to his own grave. He exhumes his own body and drives back. Once upon the mountain Johnny re-buries himself but keeps his arm. He uses his arm as the marker after scratching "Never Fade Away" on it and polishing it up a bit.
When he sticks the arm in the dirt he manipulates the hand into 'The Bird (The Middle Finger)' and faces it at Night City in the direction of Arasaka Tower. V comes back and Johnny shows him what he has done. V is actually impressed, smiles and laughs. Johnny gives him a Brotherly type of love look and actually says Thank You and bows his head and evaporates back into the Engram.
Later in game after the main story is done, if you have not completed all side jobs, gigs and still want to crack skulls you'll see the mountainside start to have graffiti on it as a tribute to Johnny. As more time passes you can go back up there and you'll see flowers and stuff around his arm. Kerry has opted to pay for round the clock private security to make sure no one steals his bandmates arm.