I think you've completed it as far as you can at the moment. If you go to deserted base, it should show that the next part isn't ready yet
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.