1. I believe the unknown signal is actually from Sylens. I believe that as he was learning/exploring the ancient knowledge when he discovered hades and realized the potential. He studied, and explored GAIA inside and out, and found a way to make the signal to make all the sub processes self aware so that he could learn all the ancient knowledge. He started going crazy for knowledge. Since APOLLO was gone(?) this was one of the only ways of obtaining the knowledge. As he said, he learned things like Calculus, etc from Hades. This also fits into how he was also able to "call" hades back to him at the very end. It also answers the question as to why he had a workshop at GAIA Prime. While he mentioned that hades never mentioned "your masters that sent the signal", I think that's Sylens being a bit of a pompous asshole. He knows full well he did it, and he's exerting dominance on hades for the kill order.
1a. Sylens also knew a lot more than he was ever letting on. I noticed twice while in the GAIA facility, when I would run to an elevator he would tell me through my focus to "watch your step" even though I wasn't close to the edge. Prior to this, before passing through a locked door, he would talk about how he tried to blast his way in for days, and could never make his way in. How would be know things like "watch your step" or things about the site layout, if he's never been in?
2. Ted Faro had access to the GAIA Prime facility because he had a back door into it which was put in without Elizabet's knowledge. I remember he was trying to get access to the back door when things first went out of control so this is not uncharacteristic. However, I am not sure how he was able to implement such a back door. He might have worked with the hades programmer or something to get it in there.
3. As much of a villian Ted Faro was, it was ironic that the Master Override which saved everyone from hades, was the result of Ted Faro. Elizabet did not want a Master Override, but Ted did and without it, all would have been lost.
4. I do not believe the ship in space blew up.
5. The entire sequence around the children in the cradle confused me. While APOLLO was deleted, what was the harm in not letting them in the door? Recall that the kids "hated" that door because they couldn't get in. However, if they could get in the area was useless anyway. Not sure what the point of sealing them in smaller quarters was. There's also the part where they ran out of food and were cast into the wilds. This is a really broken plot sequence because if things worked perfectly, but GAIA needed to reboot the world again for whatever reason, no new food would be in that place -- the cycle simply couldn't continue. I'm also confused, if you can create children, how could you not create food?
6. Even with the interviews, it's unclear where some of these people came from to make the HZD.
7. There was very little I recall about Elysium, or how others families spared. I wish there was more discussions on this matter.