Goddess Madoka eventually cleaned up this entire mess after everyone died.The Drakengard dimensional impact and the resulting magic salination and the "Gestalt" solution/Shade/Black Script situation caused a spiritual clusterkerfark of epic proportions. Fortunately the spiritual corruption was similar enough to going Witch that Goddess Madoka was able to guide them to a stable afterlife. Nier's Ret Gone of himself to save Kaine got her attention. In fact, he's one of Madoka's rare male helpers.
After ending D, the characters will find a way to remember Nier.The nature of Nier's self-Ret Gone isn't made entirely clear, but we know that he has indeed left traces of himself behind - Yonah herself couldn't really exist if Nier never existed (what with him being her father) and Kaine still gets to keep her Lunar Tear, and even remembers that it holds some sort of significance to her. Furthermore, Yonah kept a diary which frequently mentions her father, and at least one entry explicitly mentions that her father knew Kaine, so the two of them can draw the conclusion that this hole in their memories is probably related to Yonah's father. Of course, this assumes that the diary remains intact, but even without it the fact that Kaine came to rescue Yonah ought to make them both aware that they are linked somehow. Adding Emil into the mix makes it even more likely that they'll be able to piece some things together. Nier was instrumental in Emil's transformation, and his butler sent that letter to Nier before then - so without the memory of Nier, he will too need to search for an explanation for how those things came to pass. Since he clearly remembers Kaine and is trying to meet up with her, this reinforces the notion that they might go on a quest to figure out what happened to their memories. And finally, there's all the villagers. Nier ended up affecting the lives of just about everybody in the game through his actions, especially via the sidequests. A lot of people are going to suddenly forget who it was that got them the parts to fix this or grow that or forge the other. At the very least, I think that Kaine and Emil (and possibly Yonah, depending on how healthy she is) will go on a quest for answers, and considering what an impact Nier had on the world, I would be surprised if they couldn't find at least a few. Perhaps their memories alone won't be enough to call him back (this IS a Cavia game, after all), but I nonetheless think that Nier's Ret Gone is not as final as it appears. (addendum: This was written with Father Nier in mind. While some of the finer details may or may not apply to Brother Nier, the overall idea should work for him as well.)
The whole of the world explored in Nier is within a giant artificial reservation, somehow cut off from the real world.It would explain the eternal daylight and the lack of a sun in the sky. The dust that came from the Grotesquerie mother, spreading White Chlorination Syndrome, did a lot more damage to the planet than was implied. Humanity built this reservation in conjunction with Project Gestalt. Maybe it was an artificial planet, in the Earth's sky, a la Cocoon. One moderately sized landmass and oceans covering the rest of the planet. Unfortunately, it was never finished, explaining all the ruins of buildings and relics from the old world. It was supposed to be as close to the normal world as possible. Before they died out, all that remained of our species sealed themselves within until they could become one again. From there, it would simply be a matter of waiting it out until Earth is habitable again.
Tyrann is Caim's spiritLet's see, ruthless murdering psychopath who can only mentally communicate with a misanthropic badass female whose life he saved by forming a pact. How he became a shade could be a little iffy considering he was long dead before project Gestalt was created but it seems to be a world where souls exist after death and failing that his own connection to a magical alternate universe could have made it possible.
Brother Nier and Yonah are children of Father NierThe "brother" Neir of Replicant is named after his father (the "father" Nier of Gestalt). In the first scenario, Father Nier and his wife died, leaving Brother Nier and Yonah as orphans. As the game progressed, Brother Nier sacrificed his existence to save Kaine. Because he was erased, his birth never happened in the second scenario, making Yonah the only child and changing his father's fate (his mother still dies, but his father survives). Thus, the Nier of Gestalt takes over the role of Neir of Replicant. And when it comes to either sacrificing Kaine or saving her, it's most likely that this Nier performed a Mercy Kill on Kaine instead what his long-forgotten son did in the previous life. Though, there may be some little chances that father Nier might sacrifice himself, thus the cycle continues and history repeats itself.