I've tried to keep this post very light on spoilers so new players can read it to, but obviously there will be some small spoilers.
OK, I've only recently finished the game for my first two playthroughs and getting the secret (dont fear) the reaper ending was kind of annoying, so here are some things that I'd have liked to know beforehand.
my main problem was that the tutorial I watched (I assume it'll be one of the first to pop up for anyone looking) said that you just needed a friendship score of over 70% with Johnny, which to my knowledge, is just not true.
as far as I've seen, the friendship score doesn't seem to have any effect on whether you get the ending or not, tho you might want to be nice to Johnny just in case.
anyways, what you need to do to get the secret ending is basically contained to the quest 'chippin in' which is available after completing the 'tapeworm' quest, shortly before the point of no return ('meet hanako at embers.') then when doing chippin in you can basically play as you see fit, right until Johnny takes you to the oil fields. then it's important that you choose very specific dialogue choices. (I don't want to list them all here, but a tutorial should be very easy to find on YouTube or anywhere else).
after that the last thing you need to do is let Johnny take rogue to the date at silver pixel cloud (the drive in), after that you can initiate the point of no return.
then comes the roof top scene, where you get to choose which ending to take. here it is important that you select the option where you Johnny control of the body and goes with rogue, upon which he will ask you if you're absolutely sure. now, at this point you do not respond. instead you just do nothing and wait for five minutes, at which point Johnny should propose an alternative path to you, which will be the notorious (don't fear) the reaper ending.
hope this helps some new players.