So according to the various data logs Ted Faro had his own personal bunker (Thebes). The name Thebes and Elisabet's response to it (gag) is interesting. Thebes was founded by Cadmus in Greek mythology, who is famed for having spread writing and the alphabet into Greece (borrowed from the Phoenicians.) That could turn out to be important.
That brings me to the Lightkeeper Protocol. According to Elisabet's journal, the idea was to generate a clone of each of the alphas, which that alpha would raise and train, and so on, ensuring the alphas are essentially there to watch over GAIA as she rebuilds the world. Obviously Elisabet 'shot down' the protocol, but not before their genetic material was placed in the cradles, which is how we get Aloy. So whose idea was Lightkeeper anyway? Maybe Ted's?
What if at Thebes, Ted Faro built a shelter capable of supporting his own Lightkeeper protocol? He'd only have to shelter and feed two people at a time in order to make that work. Imagine that Ted Faro is still alive, in his 12th or so iteration.
Now, he deleted Apollo and killed the other alphas. But what if it wasn't about 'addition by subtraction?' what if it was really about ensuring that his cloned descendants were the Cadmus of the future, bringing out from Thebes the knowledge of humanity stored in his copy of Apollo (technically 'borrowed' from the original Alphas, like Cadmus's alphabet was borrowed from the Phoenicians)? They'd be like demigods.
What if the Ted clone sent the signal that awoke Hades, and he was planning to come out of Thebes just in time to shut Hades off again, further cementing his demigod status? Ted's eulogy for Elisabet (you got to be the Savior and the martyr…) makes me think Ted wanted to be the Savior. Now Aloy has totally screwed that up.
My thought is that Aloy will eventually have to deal with a cloned Ted Faro in the flesh. Possibly the emperor of some till now unknown civilization that is way too advanced. Maybe he's already in route, having planned to stop Hades just in time to reap the adulation from all the tribes. Aloy will have to fight him all the way back to Thebes. Reward for defeating him? The last Apollo.
Heck, I bet I even know where 'Thebes' is! California, probably silicon valley. Ted's civilization is probably responsible for the lost Sun King. 'Bold IRIV, who saw the sun passing into the west as a challenge, and forged after it with a great army…His cohort broke through, and were vanished into the lands beyond.'
What do you think?