So, Shinji gets to have his little chat with Yui. No matter how many times Shinji dies or is (re)born, she will always be watching, silently, from afar~
what happens to all his mates that were seemingly evaported omg halp
They will come back to the new world again. Though they won't know each other I guess. Shinji's rejecting Instrumentality means the primordial soup will cease to exist and all the souls (well not all, but most) will be reincarnated. They won't be the people we used to know, since this is all a kind of a reboot..
Nice touch from Gendo being the one telling Shinji to live in this new world.
Very sad chapter, if you really think about it. Now Yui is stuck in the Eva, hovering above earth forever. And Shinji finally says goodbye to his parents.