If you pause the game you need to unpause it when your Exit button is pressed. This is how Godot tree works:
&gt;Root node (Its a Node that is always there)
&gt;&gt;Your scene

So if the game is paused (your root node is paused) all your childrens are paused because the default pause mode on nodes is set to "inhereted". So you need a get_tree().paused = false on your _ready() func in your MainMenu scene in order to "fully" reset the state of your game. Another solution is:

Func on_exitbutton_pressed():
&gt;get_tree().pause = false
&gt;change_scene("your_scene")