To get johnny permanently taking v's body you'll need to reach the temperance outcome which can happen through three specific routes. Storm arasaka with rogue, team up with the aldecaldos, or execute the secret solo assault - but the key is what happens in mikoshi. When alt presents the choice, let johnny keep the body instead of reclaiming it. The actual execution is straightforward - complete your chosen assault path, then during the crucial mikoshi sequence select the dialogue options that let johnny stay in control while v's consciousness merges with alt beyond the blackwall.

After taking over, johnny leaves night city behind and starts fresh somewhere else, carrying v's memories with him. Just remember that whichever path you take - rogue's suicide run, the aldecaldo assault, or going in solo through don't fear the reaper - the critical moment comes down to that final choice in mikoshi, so be ready when it arrives.