Accessing object clones?

I am making a pause menu for my game, is there a way to set all instances of an object to "active=false;" (so I can stop all of the enemies in my game)?

To implement pause it's much easier to set the timescale to "0". If you worked with Time.deltaTime (and you should use it) everything just freezes.

You can search for game objects by name, tag, or type; using one of those methods, you should be able to acquire references to the objects in question.

If names or tags aren't an option, and if the objects in question don't all share a common component, one option would be to create a 'tag' component, the primary (or only) purpose of which is to allow you to find all objects that contain that component using FindObjectsOfType().

So in short, yes, there are several ways it can be done.