Maybe that's just the way I played, but I thought a lot of the story was directly related to the struggle of co-existence between synthetic and organic life. So many choices depended on that, from ME1 and on... everything from Kaiden's implants, to Grunt's test-tube creation, to Resurrected Implanted Shepard, to the fear of the Geth and Legion sacrificing himself to give a consciousness to his race (parallel's what Shepard does in Green ending), Jack's tortuous experimentations, Tali's endless war, EDI's giving of free will... it all had to do with the moral questions around artificial intelligence, the ethical nature of human modification, eezo, biotic implants, etc etc. It was really hit over the head with Javik - I always got the sense their clear black&white attitude toward synthetic life is what ultimately led to their destruction. The Protheans epitomized an organic-dominated galaxy with 0 tolerance toward synthetic life, and they stood no chance in their war. They did not represent an 'alternate solution' and became another failed cycle. He basically says as much to Shepard in his rant on the evil of synthetics left to themselves in this world, and all life depends on their destruction.
Javik is all like Red Rainbow, TIM is all like Blue Rainbow, and EDI/Joker are all like, Green Rainbow. Or something; but that was how I felt most of ME3, and the seeds have certainly been plated in the universe since ME1. All of that fed up to your ultimate decision, how do you view this balance, how do you personally define life, and go ahead, pick a side.
There are a lot of issues with the ending I'm now learning that I've had 24 hours to reflect, but thematically, that part makes sense to me.
and Shepard died.
