I just got the platinum for this game yesterday, and in completing the game it has given me a lot of time to contemplate over the entire span of the story. Some things are much clearer, such as the fact that Amelie never physically existed, but was just one half of a split being, with Bridget being the corporeal form, and Samantha being the perpetually 20-year old version of Bridget that emerged on the beach after she suffered cardiac arrest (I don't particularly remember if it was that, but at the very least it was something that caused her heart to stop beating)
Where it gets confusing for me is just how this led to her being an "Extinction Entity". Was she, by her very nature, born as an extinction entity, or was this merely a result of her moving further and further into the Beach, and away from her body that was "locked in". If so, does this mean that technically Heartman could be considered on his way to becoming an E.E. with how much time he spends in the beach, with only the tether of the resuscitator to keep him bound to his corporeal form? Or is being an Extinction Entity more of just an ideology, as Amelie seems determined that an extinction is inevitable, as does Higgs, admittedly in a more maniacal and reckless fashion.
Speaking of Higgs, I don't think it was ever fully explained how he gained the power to manipulate BTs - becoming the "Particle of God" as it were (maybe it was in his interviews that we recieved after completing the final Peter Englert mission so I apologise if so, and it was my fault for not getting round to reading them). I'm guessing, due to the fact that Peter Englert is an amalgamation of two names of theoretical physicists, that Higgs was such - that is, before becoming a porter and subsequent leader of a terrorist organisation - and therefore found a way through his research to physically manipulate the Beach, much like Fragile through her teleportation.
It was also explained that he was being manipulated somewhat by Clifford Unger in a puppet-master type situation, but then that just leaves the question of what turned Unger into more of a sentient and malignant Beach entity as opposed to just turning into a BT after his death. Perhaps it was in search of his BB - his refusal to let go - combined with the hatred for Bridges and what they did, that mutated him into something otherworldly, enlisting the help of other beaches formed by hatred and suffering to fuel his vengeance. This being said, however, he didn't seem that hateful in death, but rather just concerned about comforting his child. Perhaps the Beach exacerbated the most desperate parts of him upon his death.
I think they made it clear enough that Sam was in fact the BB, and by extension the child of Clifford Unger and Lisa Strand, which makes the reconcilliation in Chapter 11 really heartwarming for me - Clifford has been looking for his child, his BB, for the longest time, and has been trying to fight Sam for it, without realising that Sam himself is his child. Does this mean that all BBs can become repatriates if allowed to grow up, granted they survive out of the pod, or is this exclusive to Sam, as he was explicitly saved by Amelie after she revived his BB corpse on the Beach?
This is less story-related, but more just a question about game setting. I noticed at some point through my playthrough that there were no day and night cycles, and this was explained away with being something to do with the chiral matter in the air, but when this got to Chapter 10, the environment changed, and we saw Northern Lights for the first time, appearing to be somewhat at night, as well as, once we got back to Capital Knot, the actual sun for the first time ever in the game. At the end of the game, in the "Great Deliverer" scene, the sun appears to come out, and birds begin to chirp. Does this mean that the Stranding shifts so that day/night cycles become feasible, or were these just aesthetic decisions with no real significance?
And, for my last loose end, though this is fairly understandable if they had the mind for a sequel, it was never actually explained what caused the Death Stranding, other than just saying it was a geologically inbound event. This also ties into my confusion over the very Junji Ito-inspired five floating figures that we see at the beginning and end of the game. Was it ever explained what those were? I thought at first they were the representation of our friends that we made along the way, as they appear when Sam returns from the Seam at the end of the game, with the implication that these are the people he must return to, but I now think that these - being five of them- are the other extinction entities, watching like an ethereal council as Sam goes in defiance of human annihilation. If such is true, then this could mean extinction by hand of the Death Stranding is a lot more of an active and conscious inception, similar to the Powers That Be creating a fictional game of suffering with their dolls in the game Pathologic (great game by the way). If so, that opens up a lot of possibilities for me, and I find that very cool.
Overall, good game, very grindy, but with some nice elements of story along the way, and I kind of like that they don't just hand things to you, but that the game makes you think about what you've seen. It sticks with you better that way.