Shu used his Gai void power to Bring EVE out of Inori, since that's the only way he could be with her-he took the seat as king and made Inori INTO EVE-remember Inori was a copy of Mona, and had the EVE power to remake the world within her-Shu just needed Gai's power to bring it out of her. Inori was still existing though and came to Shu. This is where people miss the point, Shu had the king's power and could create the new humanity but EVE was gone. Having that Shu basically had Inori's soul. Inori was preserved genetically with her last tear that dropped and crystallized as the flower Shu took hold of. Shu could have created a new world but with Mana's body gone there was no person to house the EVE creation power, but Inori was the whole time created solely to house the EVE power. Eve represents the potential to create a new world. However, since Shu was absorbing all the voids he took Gai's void power, his king power. In the end Gai went to Mana's traumatized body before the lost Christmas event to be with her to save Shu's sister but they both died.

Remember when Mana talked to Shu about Triton looking at her? Triton liked her and still did to the end. In the end Gai wanted to save Mana, Shu's sister, because he couldn't care less about anyone else and was willing to sacrifice all of humanity to be with her. Shu's selfless nature and Inoris innocence represent the opposition to this. Shu's battle is against the selfish, survival of the fittest 'natural selection' of human nature represented by Gai and Mana-who only seek to reproduce themselves, also Doth who represents the natural drive of reproduction.

Shu and Inori are thesis and Gai and Mana are anti-thesis. Thesis is the main message of the story, anti-thesis is the narrative tool to highlight thesis, using Protagonist and Antagonists to represent these ideas. To understand what happened you have to think like the writer, and what thematic point they're making. Seems vague but after reading several discussions on forums I think I can break it down and explain the reality I haven't seen anyone else come to: Just watched this anime and the ending, like everyone else had me confused and bothered.

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