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Is there a way to have the plugin start disabled and remain disabled until I use a plugin command to change it? 

I'm aware that  it can be toggled off but that is only until the player travels to a new map and it gets reset to enabled every time.

This makes me unable to use the plugin because only a few certain sections of my game will be rendered in 3D and I can't seem to find a way to have it remained disabled conveniently until I need it without using extremely tedious eventing in every single map to make sure it's off. 

(+1)

Sorry for the late response, in the plugin parameters you can set up the default settings for maps. If you disable it there, then it will be disabled for every map until you turn it on.