Abridged Full Story:

Link is called to a land neighboring Hyrule to fight Ganon, exploring three different time periods centuries apart. Many locations exist in all three time periods, including six dungeons and a town in unrelated peril. Ganon has found a way into the magic bunker, and the only way to enter is with a set of six blue Tears. Link is tasked by the white mage to explore each dungeon in three time periods, collecting a blue Tear from each of the six. Along the way (and all optional), Link chooses a character class, frees the town from evil wizards, and even conquers the arena prompting the town to gild the statue.

Now that Link has all six Tears, he enters the bunker in the future. He finally reaches Ganon in the past. Link defeats Ganon easily, and Ganon drops a second set of six Tears arranged in a circle. Link picks it up, and finds a hole blown in the back of the bunker leading to the mountains. Nothing left to do but plug the hole, and as Link pushes a nearby boulder in, a path opens up.

Link goes into the white mage's temple, who tells a story of how a second key was accidentally made, and hidden out of embarassment. He takes both keys before noticing some things that got lost in translation over the centuries since the bunker's seal was made. The supposed Tears were actually torn petals of the order's symbol, a blue corn flower. The name Chronos must be a misspelling from "The Corns", which is what the locals called them behind their backs. But in our language "the torn cornflower" sounds stupid. The white mage will keep the one key with him, and scatter the other key across the land. And that's the end of the game.

The final challenges appear in the overworld, four secret dungeons (combat, blind maze, puzzle rooms, lost woods) that didn't previously exist, and a cave that needs all four. So Link completes these four challenges. He finds that cave in the future leading to a fifth secret dungeon, which is the abandoned castle of the town. Link wins the final battle here, for the secret ending of the game. Now, it's time for you to see what really occured, unbeknownst to Link.

You learn that there was no second set of tears. Link was tricked into making a time travel duplicate. Link brought the key he collected from dungeons in the present and future to the white mage in the past. The white mage scattered Ganon's key, while keeping the key Link collected. If Link or Ganon found out about the duplicate, they might try to exploit it, so the white mage lied. The time continuum is maintained with only a single key ever being created. So what if the key the white mage (whoever he/it is) holds on to is several centuries older than the rest of the world; inanimate objects are hardly in a position to complain.


Full Story In case you want to read the longer version, including individual dungeons and events. Quite a bit longer.

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