Render is completely transparent I've checked the active camera, there's nothing in the sequence editor, I've tried everything and cannot figure out what I broke. 

I literally just want it to render out how it looks in the viewport a Smoking crashed spaceship against a green screen. But for some reason, the render is blank, and then also it puts the video clip from the motion track on it too, which I don't want it to do either but that's a different issue.

Viewport:

Node tree:

Notice how the initial render is completely blank...?
The issue you are having is that the layers you have set your Render Layers to are completely blank in front of the camera. You need to add the correct layers in your Render Layers settings.




The reason this was rendering in the viewport, is you had all of the layers selected to display in your viewport, while those layers were not enabled in the final render.



You may want to disable the compositing stage to get ride of the video overlay :



to keep the compositing and just eliminate the video overlay change the compositing nodes as this :