The story borrows heavily from Romeo and Juliet for sure, maybe a bit of Jesus story too ("chosen one", reviving the dead etc)
What irked me the most is actually the resolution of the story. Nefaryus going from evil emperor to happy ruler almost on a whim kinda undermines the character I feel.
I think the Biblical story it owes the most to is that of David and Jonathan, with Gabriel as David, Faythe as Jonathan, and Nafaryus as Saul.
David starts off in the court of King Saul as a musician of great talent, the only one capable of soothing the King. After David kills Goliath and performs some other feats, he becomes extremely popular with the people. Saul becomes jealous of David's popularity and sees him as a threat and tries to have him killed. Eventually, he forces David into exile, where the political situation gets super messy.
Meanwhile, Saul's eldest son Jonathan becomes David's closest friend, to his father's displeasure. He is the one who warns David of Saul's intentions before David escapes, and even in the face of talk of rebellion, their relationship stays strong.
The ending is very different, as Jonathan and two of Jonathan's younger brothers are killed in battle (not against David), Saul kills himself rather than facing capture, and David becomes King. And of course, Faythe is female and the romantic subtext some see between David and Jonathan becomes textual.
But I can't stop myself from seeing Nefaryus as Ian McShane from the 2009 series
Kings, which was based on the same story.