Hey guys,
So I just blew up the Military Base(gives me the cut scene and everything), and it immediately sent me back to the title screen. Im just trying to figure out why it continues to do this, as if I load my most recent save game (The one I used pre base destruction) it just has me go through the whole procedure again. I have not yet gone to the Cathedral and dealt with the master either, which should mean that I can go and move freely about.

When I blew up the base the first time I stayed outside the perimeter fence to watch the explosion. That resulted in being sent back to the title screen.

The next time I left the area completely. That allowed me to watch cutscenes and then continue to the Cathedral.

Yep, you need to leave the area.
You have to touch the red "shadow", OP.