Zone 1,2,and 3 are all purified already, as the game will now take place after the Judge special ending. Sucre, being unfought by the batter, but being aware of his influence, convinces the Judge to come with her to see if there are any signs of life left. 

In their journey, they come across two separate zones that were safe from harm, as in his mission, The Batter only needed to find a way to reach The Queen and by extension, the switch to complete his mission. 

In this failure, these almost forgotten about zones were never killed off, but have grown wary and nervous of visitors due to the threat that took the major zones down.