I think there's a fantastic parallel here to the Zelda series. Though there exists an official (and humorously bifurcated) "timeline" that determines where each game takes place chronologically, the fundamental premise, set pieces, and objectives of most of the games all echo each other. Rather than trying to fit all of these games into a linear narrative, I think it's more fun to think of each game in the Zelda series as a retelling of the exact same story, much as real-world legends change subtly over time as they are passed down through generations and across cultures.