I want to make a global variable that contains a reference to an instantiated scene (an enemy that is being selected).

I went into the project settings to add a new global property but none of the datatypes shown in the drop down list look like it'd be suitable for storing a reference to a node. Any ideas? Or do I have to auto-load a script?

A var is a Variant, and can hold any valid value. So if you do this:

var blue = get_node("blue_enemy")

Then it will be a reference to that node. Or if you create it in code.

var blue = blue_enemy_scene.instance()

Then you can save blue somewhere, in an Array, pass it to a function, whatever.

    You should use an Autoload for this. Then you can define any variables you like.