My memory says:
1. Beat game, get the whole star deal and get told to keep playing to get the good end.
2. This is the fuzzy part. When you start up again, your “go here” indicator is on the final dungeon, but I THINK you’re supposed to go back to either headquarters or the area where the mutant humans live to get a quest concerning Natasha’s (I think that’s her name) condition, which takes you to a door you couldn’t get through in a previous dungeon. The map will indicate the final dungeon is your destination until you’ve done this dungeon.
3. I think that after you do that, the interface works normally as far as the map screen pointing you where you need to be going. I can’t remember all the details, but I know it was a bit tricky to figure out what to do at the beginning because the game didn’t really help at all. I know you re-fight the main game final boss fight, like you do with most ExeCreate games, in the post-game, but you don’t start out with him. You do something else, then go to him, then do the rest of the post-game.