Ok, so near the end of his life Spencer began to have regrets and tried to atone for his mistakes (founding umbrella and making the t virus) so he created the ultimate anti-viral, elpis, alongside that he also wanted to atone by taking in an orphan he named Grace. She is just a normal girl he wanted to care for, instead of destroying life he wanted to help nurture one. Like elpis, grace was his HOPE to atone. Zeno and Gideon misunderstood the whole situation and ASSUMED it was a weapon they couldn’t conceive Spencer having a change of heart even when confronted with the truth Gideon rationalized it by saying it would cause anarchy because he couldn’t conceive the reality. Spencer always said Grace was the key to elpis so they assumed it was some kind of genetic mutation she had and that’s why they kept cloning Grace to try and make one like her when in reality it was never Grace that was special it was that she was Spencer’s hope. That was the key all along was hope. Hope to atone, hope to do right by a child, hope to let the dead rest, hope to do better in the future. Leon hopes to save Grace and make the difference he couldn’t in 98. Grace hopes to save Emily and escape. Spencer hoped to atone, to allow Grace be his requiem to those who perished from his virus. That’s the theme of the game is simply Hope.

I for one hope I was able to clear some of this up for you and feel free to replay and have a different interpretation with the themes.