The Legend of Zelda: Sacred Reliquary

Legend of Zelda: Sacred Reliquary is a Zelda fanfic by Sharper Than the Sword. It takes place during an undisclosed time during the history of Hyrule, and incorporates elements of all the games in unique ways. Characters from throughout the series show up in large roles or just as characters to fill in a given spot, but on the whole this is a unique take on The Legend of Zelda.

For starters... Instead of being Black and White Morality, it's decidedly more muddied. Hyrule Castle and the city surrounding it have grown immensely, and ruling over it all is Princess Zelda, a cold and aloof leader who many call a tyrant for allowing various cruelties to take place. Meanwhile, Ganondorf and his band of thieves and thugs try to bring change to the city, but do so in some unsavory ways.

Link finds himself caught in the middle of all of it, trying to find a way to stay true to himself and slowly being dragged into the fight.

Tropes found in both Sacred Reliquary:

 * Action Girl: Ashei, Tetra.
 * Bag of Holding: Link's got one, natch.
 * Big Bad: Zelda, surprisingly. And interestingly enough, she's presented as somewhat of a Well-Intentioned Extremist with a bit of The Social Darwinist thrown in.
 * Call to Adventure: Link doesn't so much get a call, as he gets kidnapped and pressed into service after being saved from an Eldritch Abomination.
 * Crapsack World: Hyrule.
 * Dark Action Girl: Zelda, Midna.
 * Darker and Edgier: than any Zelda game. Even Twilight Princess and Majora's Mask.
 * Dark-Skinned Redhead: Ganondorf and Midna.
 * Despotism Justifies the Means: Zelda.
 * The Dragon: Rusl fills this role to Zelda. Vaati and Zant also seem to be in on the fun as Zelda's advisors.
 * Eldritch Abomination: One stalks the streets of Hyrule at night.
 * Everything's Better With Princesses: Or in this case, very much not.
 * Evil Me Scares Me: Ganondorf is very against what his past lives have done.
 * Evil Tower of Ominousness: Zelda's own palace has a few.
 * Fairy Companion: Navi, of course. With Stop Helping Me in full effect.
 * Fate Worse Than Death: "Get out."
 * Fridge Brilliance: The switch in plot position of Zelda and Ganondorf makes a lot of sense in this story: Zelda used the wisdom she gained from her Triforce piece to amass great amounts of magical and political power. Ganondorf, meanwhile, found that the power he had from his Triforce piece wasn't enough to save his people, and thus gained wisdom. So even though they haven't switched Triforce pieces, they've gained a measure of what the other is generally noted for.
 * Great Escape: The rooftop chase as Rusl attempts to cut down Link.
 * I Am Who?: Unlike Zelda and Ganondorf, Link had no idea he was a triforce bearer when he arrived in the city.
 * Jerk With a Heart of Gold: Midna would certainly qualify.
 * Lady of War: Zelda.
 * Last of His Kind:
 * Manic Pixie Dream Girl: Midna, surprisingly enough, carries elements of this in the story towards Link.
 * One Head Taller: Midna to Link, in her natural form.
 * Pint-Sized Powerhouse: It becomes a plot point with
 * Shout Out: Plenty to games within the series. Minor characters are often named after characters throughout the games, often serving similar (but not identical) roles to the ones they played in the games.
 * Stop Helping Me: Navi is no longer allowed to help out the Gerudo for a reason.
 * Treacherous Advisor
 * What If: Essentially the driving force behind the story seems to be: What if it was the Triforce of Wisdom which corrupted the bearer instead of the Triforce of Power?