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The True Zelda Backstory, v 1.2
In the beginning, the universe was created.
On one planet was the Mushroom Kingdom, where the legendary Plumber had many adventures. In the events of Super Mario Galaxy, however, the universe was damaged beyond repair, and the planets and galaxies fell into a singularity. With one massive explosion, the universe was reborn anew – planets and all!
Hyrule's planet was one such newborn after the ending events of SMG. Also, the Metroid planets. You can tell the Zelda planet is rather small, just like the SMG planets, because of how quickly day and night alternate in Ocarina of Time and Majora's Mask. Small planet = quicker rotation.
Rosalina, the star princess in Super Mario Galaxy, descends upon early Hyrule and gives its people technology and three corners of a magical Mario star, which form themselves into the Triforce. The Triforce hides away in the Sacred Realm, which is a parallel world linked to Hyrule's planet. You know, sort of like those weird doors in Super Mario 2 that you can enter and get coins from. It's Mario logic. Stop thinking.
She then leaves, continuing her roaming throughout the Galaxy in her spaceship. Religious splintering throughout Hyrule's ages and the passage of time transforms the legendary figure of Rosalina into the popular image of the three goddesses – each one representing a different aspect of her.
The aliens in Majora's Mask are an evolved form of the Lumas seen in SMG, and they are responsible for safely advancing the planets of the new galaxies. Also responsible for stealing cows, for reasons unknown.
She leaves behind a strong legacy. Princess Zelda is from a long line of royals claiming descent from her. This is obviously true, as they both have blonde hair, blue eyes, and are princesses. Her semi-divine background is the reason she is the Princess of Destiny. It also accounts for her telekinesis, as Rosalina could fly and stuff.
(Princess of Destiny. Blonde, blue eyed, telekinetic - it's not just a coincidence!)
Ganondorf arrives and gets to the Triforce, and turns into the big bad we're all familiar with. And does all his evil stuff. Before the Mario-Triforce-star's invincibility/catchy song wears off, Ganondorf discovers the Villain Resurrection Device ™, left behind by Bowser before the creation of the new universe. This is how all Nintendo villains avoid permanent death even though the heroes kill them repeatedly throughout the years.
Link kills Ganon. Ganon is subsequently respawned. Again and again and again, just like Bowser was. The cycle continues for eons. You know. "This has all happened before, and it will all happen again."
(Ganondorf comforted after rebirth at the Villain Resurrection Hub - each rebirth hurts just a little more.)
IN THE FAR FUTURE....
On other planets within the Super Mario Galaxy universe, Samus Aran, a bounty hunter, must save the new universe from the Space Pirates and the Metroid species. Technology has rapidly advanced, so people can travel throughout the galaxy via spaceships rather than Mario stars and mushrooms and whatever other vehicles all those crazy space Italians used back in the day.
Samus is another descendant of Rosalina, given her special destiny and the fact that she is also blonde and blue eyed and is otherwise awesome. She may or may not be related to Zelda, depending on whether Hyrule advanced so much that it became responsible for the colonization of other planets.
(Bounty Hunter of Destiny.)
Ridley has also discovered Bowser's Villain Resurrection Device ™, and makes use of it. The cycle repeats again!
(Meta-Ridley resurrecting at the Villain Resurrection Hub - now controlled by Space Pirates rather than Ganon's dark forces.)
The conclusion of the Metroid saga will result in Samus using Zelda's Medley to return to the Mushroom Kingdom planet, where she will finally destroy the Villain Resurrection Device ™, and restore permanent order to the universe.
So yeah. That's the real timeline.
