What happens if I try to continue my existing game after I beat Bastion?
EDITED: After a bit of clarification in the comment, and a quick test, a slightly modified answer.
On your second play-through in "New Game Plus" mode, once you get to the point where it says you won't be able to go back, it will act like the first playthrough, in that you have to continue through to end the game. However, when you are finished with the game and after rolling the credits, you can Continue your story from the main menu. It will take you back to the Bastion before you entered the final zone. So, 1. The game dumps me in the Bastion right before I entered the zone, allowing me to play through the other areas some more. is the answer you're looking for.
DISCLAIMER: On my New Game Plus, I chose "Evacuation" as the end game choice. I do not know if this has any bearing on being able to continue or not.
That being said, you can do really go either route:
- Beat the game, and you then continue and beat the Vigils, or
- You can not beat the game, and complete any remaining Vigils to get that achievement, complete the Who Knows Where areas as you mentioned, do anything else, then when you're ready, complete the game to finish it off and get the last achievements.
If you're looking for a suggestion, I would go with #2, complete any other achievements you need to, and then finish up and make the other choice that you didn't make in the first playthrough which will net you with another achievement.
One thing I am unsure on is whether or not when you continue the Story after beating the game is if any experience you earned in the final zone carries over with you. I did not track this.