So, the Beast is dead. Finally. Protector of the Source....
It spawned Number Nine, a Machine, which ends his conversation about how we are doomed, how they are coming. It certainly explains the whole thing. The Aliens are coming because they fear our presence with the source, they are coming to stop us getting control over the source.
However, we are still left with a question....what exactly happened to Pandemonium, and how did the beast come to be? I had hoped we would been told this, but alas..