After reaching Mikoshi and logging into the cyberspace with the help of Alt Cunninghams Engramm after playing through this "event" I was able to make two choices (or was it three?), what I AS AN ENGRAMM of myself, could do from then onward.
1. I could offer my body for Johnnys Engramm and leave with alt behind the black wall
2. I could try to kill myself (a bit before this scene if I remember correctly (with the pills offered by Misty)
3. I could take over my old body and continue to live "my" life. But with Alt telling me, that I probably will only last for more or less another six months at max.
I went for choice 3, granting Johnnys wish to go with Alt behind the black wall and for me to go back to my old body as an Engramm.
Then I left Night City, together with Judy, my Romance and with my new family the Aldecaldos (at least with Mitch
) , leading them together with Panam into the Badlands, free! Where I also said, in a talk with Panam, that we will find a cure and she said, they got connections to help me.
In the very end, as the credits roll and the people you met (and completed the quests of) were shown with their own little video sequence. In there Misty lays my cards a last time, where she prophecised me a long and happy life after.