A/N: This is the story I wrote for the (sadly collapsed) 2017 Zelgan Big Bang. It doesn't have an illustration and as far as I know only one other story made it to completion. :(
This work is actually an inversion of my ganlink story Identities, that is to say this is what would have happened had Ganondorf lost the battle at the end of Twilight Princess. In this story, Link and Midna leave Hyrule for the Twilight Realm, and thus do not appear at all apart from a small mention in the first chapter. So yes, the Link for this story is female but that shouldn't matter because she literally has no bearing on the story (aside from shoving a blade in Ganny's chest). There is a midlink prequel to this story, but it is adult in nature and can be read on AO3.
The only characters from Identities that are shared between the stories are Aveil and Kona. Everyone else has character development that differs between the two. Kona's daughter is a prominent supporting character in this story, she is mentioned in passing in the other story.
The final battle was over. The Twilight had receded, Zant was no more, and the evil being that had supplied his power was impaled on the Master Sword, never to threaten Hyrule again. All that remained was the matter of the Twilight Princess, and as it turned out, the crafty imp had survived Ganondorf's attack and now stood in her true form, free of the curse that had plagued her for so long.
Zelda stood at the base of the hill and watched as Link reunited with Midna, the two of them overflowing with joy at finally being together. Seeing as it was not her place to spy, Zelda turned from the happy couple to the grim figure looming just over her shoulder.
Ganondorf had not died the moment Link impaled him, but rather when the Triforce of Power seemingly abandoned him. Why would it do that? Zelda thought, as she studied the giant man. Furthermore, as she had watched the battle it became clear to her that Link was not the great fighter she had originally assumed, and that Ganondorf even appeared to be throwing the fight. How could this man go through so much, only to give up in the end?
Curiously, Zelda found herself gripping the Master Sword and slowly withdrawing it from the crack in Ganondorf's chest. She had to brace herself against his armor, and her glove quickly stained with his blood, but she removed the blade without further assistance.
At that moment, the sound of Link and Midna warping away startled her, and she reflexively drew her palm to her chest. Sighing when she realized the unflattering blood stain it left behind, she cast the Master Sword away into the dirt and began mumbling to herself. "Oh, what was I even doing..."
Suddenly, Ganondorf let out a strangled gasp and fell to his knees, grabbing Zelda's shoulder and wheezing while she screamed in panic. When Zelda tried to wrench free of his grip, it knocked him off balance and caused him to collapse on top of her.
"Great Golden Goddesses! Link, someone, HELP!" Zelda squirmed and thrashed, but the Gerudo was too heavy to push off. Link was gone, and no one around could hear her pleas. Oddly enough, Ganondorf had fallen back into unconsciousness and was not trapping her of his own accord. Unfortunately, he must have weighed in the neighborhood of three hundred pounds, and not even Zelda's secret Sheikah training was enough to move him. She did not know any spells that could teleport without an instrument to channel through, and in her panic, she did not think to call the Light Spirits for help.
Zelda squirmed beneath him for what seemed like hours, until Ganondorf started coming around. She froze in horror as she watched the desert king grimace, then crack his neck, before finally opening his eyes.
"...Queen Zelda." Ganondorf rose an eyebrow in confusion as Zelda meekly nodded, then turned his head to the left and right to scan the area before settling back on her. He did not seem the least bit concerned that he was lying atop Hyrule's queen. "Where did the girl go?"
Zelda returned an equally confused stare, so Ganondorf decided his own investigation would produce better results. He attempted to stand, but found there was no energy in his body to do so. With a grunt of pain, he managed to roll onto his back, freeing Zelda from her stiff and heavy prison.
The second she was free, Zelda scrambled to her feet and dove for the Master Sword, grabbing it and pointing it out in front of her as a warning. "Stay back! Stay BACK!"
"Simple chit, did you not just see how painful it was for me to roll over? And you think I'm going to leap up and ravage you?" Ganondorf rolled his eyes, and winced as he discovered just how little energy his freshly revived body contained.
"I've had you in my head once," Zelda snapped, "an experience I'd prefer not to repeat!"
"I don't repeat."
Zelda huffed, and gripped the sword tighter. Sore and stiff herself from the ridiculous position she was forced to lie in, she used the opportunity to rest as she gathered a little information. "How are you alive? And why did you let Link ki... beat you?" She thought better of her words, after all Link could not have killed him if he was here talking to her.
"As for the first question, your guess is as good as mine," Ganondorf sighed, weakly lifting his hand to see that the Triforce no longer shined from the back of his palm. "The second, well, even you should have felt sorry for her. It's your fault she was such a pitiful sad sack, it's obvious your culture made her feel she had to play pretend to save you. I couldn't bring myself to kill a kid who never got to live her life to the fullest. I'm guessing she ran off with the imp? Hope they're happy together."
"What?!" Zelda lowered the Master Sword in shock. "A girl? You... you're lying to me..."
"Lying? What cause do I have to lie?" Ganondorf began laughing, an eerie sound that made Zelda shiver. "Your hero was a woman, didn't you see it when you rode behind her on that horse, or when you shared the imp's consciousness? She reminded me of a Gerudo in some ways, insanely loyal and a warrior to the bone. Maybe that's why I couldn't do it..."
Zelda watched with curiosity as Ganondorf began clumsily stripping his armor, tossing it every which way as he laid in the dirt and sighing as his sore muscles were freed from their confinement. "So what's to become of me now, Your Majesty? You gonna drag me in front of the townsfolk for another public execution? Toss me in a jail cell to rot? Leave me out here until I recover and start the cycle all over again?"
What am I going to do with him? Zelda thought to herself. "...You were correct when you said Link will probably accompany Midna back to the Twilight Realm," she replied, choosing to address the subject of Link's gender during her own meditation later. "I could lock you up, but I do not believe that would be of any help to the rebuilding of Hyrule."
"Well then, what are you going to do with me?" he snorted as he threw away his breastplate.
A thought occurred to Zelda, and it made her chuckle with delight. "There are a good many people who think it is not wise for me to rule as queen on my own. I think that is rubbish. However, since the Sheikah attendant I had as a child has unfortunately moved on from this world, I am slightly vulnerable. There is also the fact that with your piece of the Triforce having deserted you, and Link surely going with Midna to the Twilight Realm, my piece of the Triforce is the only one left in Hyrule for you to covet. Therefore, it is in your best interests, Gerudo King, to act as my royal guardian. Once you've recovered, of course."
Ganondorf turned and looked at Zelda as though she had grown a second head. "That is the most RIDICULOUS thing I have ever heard in my life! Have you gone mad?"
Raising the Master Sword, she answered, "I could just put this back where I found it..."
"No, no!" Ganondorf put his hands up in surrender, and sighed. "How foolish you are. What is to stop me from killing you in your sleep, or planning a coup against you?"
"For starters, without your Triforce, you are vulnerable." For extra emphasis, Zelda came closer with the Master Sword and traced the ground next to his shoulder. Ganondorf tried to hide it, but it was obvious the proximity from the sword was causing him pain. "If I keep this sword with me, and have my light arrows handy, I shall always have something with which to conquer you."
"How joyous."
"Quite. Next, I will have another guardian who can thwart your misdeeds. I actually have a young woman from Termina who is training for the position," Zelda explained. "And I believe she will delight in keeping you in your place."
"And why is that?" This caught Ganondorf's interest, and he managed to prop his head on his arm to look Zelda in the face.
"Oh, because she is a young Gerudo."
"WHAT?!" Ganondorf balked at the notion of a Gerudo in service to the Queen of Hyrule.
"And the Termina Gerudo do not believe in that silly 'lone male is king' superstition," Zelda taunted with glee. "So she will gladly remind you when you are not respecting your Queen."
By now, the sun was high in the noon sky, and soldiers from the castle had come out to search for Zelda. Upon spotting her, they rode over with haste. "Ah, excellent timing. Men, I'll need you to drag this guest back to the castle," she explained, chuckling as Ganondorf growled in contempt. "Take him first to the stable and have them hose him down. Leave all the armor out here, he will not be needing it."
"The HELL I won't!"
The nervous captain of the guard averted his eyes from Zelda's bloody dress as he acknowledged the orders. "What do we do with him... afterward?"
"Oh, put him in a guest room, I suppose." Realizing why no one was looking at her directly, Zelda returned to Ganondorf and purloined his cape, wrapping it around her shoulders and hiding the blood. "If he bites, stick him with this." She handed the captain a light arrow, before confiscating the Sage's Sword and galloping away on one of the soldier's horses.