You should never, ever have to break the loop until the game ends. Literally every modern program that doesn't blow stuff runs under one, singular, loop. Chrome doesn't break the loop to open tabs in other processes, skype doesn't need to break the loop to call someone, sublime text doesn't need to break the loop to open a new project, and steam doesn't need to break the loop to install a new game.
There's no reason for you to need to break the loop to "continue the story".