Missable? (Spoilers)

So... I'm trying to get the platinum for Nier Automata and all endings, cause I liked the game a lot. I don't have much left at this point, I was going for the 95% unit data to max up my last pod, when a quest popped up at the commercial facility. Emil's determination, which I hadn't read anything about, cause I'm trying to stay spoiler-free. Followed him to the desert, and beat his clones, and I thought it would trigger an ending but didn't. Saved afterwards cause... Well, just beat a level 99 boss. Just read online that I have to let that last one self destruct to get ending Y so... Am I f*****? Is there any way to trigger it again? I thought there weren't any missable things in this game, with chapter select an all. D':

P.s.: just re read what I wrote checking for typos. Damn I was so stupid. Just didn't expect there was a missable ending. Help me out pretty please?

Edit: yes, my other saves are so far behind.