Thats odd, since i never encountered the boss on the top floor and returning to the deserted base does nothing, except i now seem to have access the parasite core room
Weird. You're supposed to get into the elevator at the top, and fight a boss battle in there. If that's not triggering, then something is screwed up with your save file. If you have RPG maker mv, you can try opening up the game and figuring out what switches you need to reset. But otherwise, you'll have to do a NG+ to fix it, unfortunately.