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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