So, to get the secret ending, you have to have a very specific series of chats with Johnny in the oil field scene. If you don't it never appears.
In the scene on the roof at the end of Nocture OP55N1 where Misty brings you so you can choose which ending to pursue, if you just don't answer which ending to pursue, after about 5 minutes of silence, Johnny will suggest an alternate approach (but only if you had the exact conversation earlier in the game).
This starts the mission "Don't Fear the Reaper".
Essentially, it is a suicide run, storming in through the front doors of Arasaka tower alone.
During this mission you mean very strong resistance, and it only grows the further you get along. You cannot save (with one exception where there is an autosave once you travel with an elevator)
If you die, you go directly to end credits, and have to reload a save in Nocturne OP55N1 again, and wait 5 minutes for the dialogue option to appear again, etc. etc.
What makes it even harder is that every couple of minutes you have another relic malfunction, that reduces your total health above which you cannot heal, resulting in many opponents being able to insta-kill you, even if you have maxed out armor that is fully upgraded, and you are leveled very high.
I have gotten really close to what I think is the end, but then I met **** near overwhelming resistance in close quarters.
I think using a System Reset quickhack on them at that point could probably take out most of them as they are so close together, but I got instakilled before I could deploy it.
I'm going to keep trying. I don't give up that easily.