>>713947223>Bridget/Amelie has her soul split from her body at 20, becoming the extinction entity>Tries to harness connection to Beach to build chiral network and unite America>Accidentally kills Sam as a baby, so she finds him on the Beach and makes him a repatriate (essentially immortal)>At some point realizes her body is too weak to finish her project and that extinction is inevitable, so she decides to hurry the process up>Enlists Higgs and the Homo Demens to play the antagonist and prod you into spreading the network (which I think further connects the real world to the Beach)>Also specifically tells you to go find her at the start, "I'll be waiting on the Beach," because she asked you to stop her in the distant past if she goes nutso mode>Culminates with Sam refusing to let Bridget/Amelie go or kill her either, so she just forcibly severs her connection to everything to stall extinction as long as possible so she's basically in limbo for eternity now>Sam winds up practically cured of his aphenphosmphobia (fear of being touched), but he's still emotionally closed off which is also compounded by the fact he spent an unknown amount of time on the Beach where time moves much, much faster than on Earth>Rips Lou (the BB) out of the pod, goes off the grid, and they live happily ever after until DS2Those are the really big plot points because I'm assuming the lore recap you watched covered all the side character stuff.
In this universe extinction is a kind of supernatural force that imposes its will on the dominant species of the era, and it acts through a chosen 'extinction entity' which Bridget/Amelie is.
The Beach is a kind of metaphysical afterlife, but you can and do go there physically. When Sam dies, though, he goes to the Seam which is like the in-between stage and then he's spat back out. Also, because of the presence of the Beach in the aftermath of the Death Stranding people called DOOMS sufferers have begun to emerge with supernatural abilities.