Author's Notes:
-This is the first real oneshot I've ever done. Let me know what you think.
-Obviously there are several ways that you (playing Breath of the Wild) could have gone through the Yiga Clan hideout. This one involves the first guard surviving and everyone else killed.
Now let's get going with this story shall we?
It was a sad day for the Yiga clan. Master Kohga had been killed by the Hero of Hyrule, Link. Deep in the lower levels of the Yiga Clan Hideout, a girl with long black hair in a red Sheikah outfit with a sword pin on her suit stood beside the fallen Yiga clan member. This was Lieutenant Karai, Kohga's successor. Master Kohga's dead body lay still in a casket, with Karai and numerous Yiga clan members gathered around him.
"Let us remember this day. Master Kohga has been ruthlessly killed by Link, our archenemy whom we have tried so hard to hunt down and destroy. You will now hear a speech from our new master, Mistress Karai." the undertaker announced.
She stepped up to the podium. She looked very angry and dissatisfied. "To the one Yiga Swordman who guarded the hideout and still lives, come forth!"
Reluctantly, he stepped forward. He bowed down to her not only in respect, but also in fear. "Yes, Mistress Karai?"
"What happened to your fellow guard swordsman? Why am I seeing not only the demise of our beloved Master Kohga, but also the death of six of your fellow swordsman?!"
"I... I don't know! All I remember is that I saw a bunch of bananas, so I picked them up and started eating them. By the time I finished them, I heard screaming. I ran to find my fellow Yiga swordmen dead and I heard the sound of Master Kohga's screaming before I heard a big thud."
"You're the first guard. You are supposed to be the top of your rank!" She sighed. "At least we still have the Thunder Helm."
Suddenly another Yiga clan member ran in, a woman with brown hair. There was a visible scratch on her left cheek. "Mistress Karai. I have bad news. The Thunder Helm is gone and so is the Gerudo guard!"
"What?!" She glared at the Yiga Swordsman. "You incompetent idiots!" She turned to the messenger. "What happened to your mask?"
"It was ripped off my face after Link broke in, then I was unconscious for over an hour. I tried to stop him, but he was too fast. What do we do now?"
Karai breathed in. "First order of business, punish the man who let this happen."
"What?!"
"Take him to the pit."
His fellow soldiers grabbed him, and took him to the pit.
"But please, mistress, I've done nothing wrong!" Mistress Karai ignored his cries and he was tossed into the pit. "Ahh!"
Eventually a large thud was heard. A few seconds of silence lingered before Karai spoke again. "Now for my next command, we have to leave this place at once. Link and the Gerudo soldier escaped. They'll eventually run back to Chief Riju and tell her where we're hiding."
"But men are forbidden from entering. That's why Master Kohga had sent a trio of women to steal the Thunder Helm." a male Yiga footsoldier corrected.
Mistress Karai looked at him, acknowledging his words. "That may be true, but who else sent for him to come here?"
"It's possible that she may have met with him outside the walls of Gerudo Town." the messenger suggested.
"Either way, Lady Riju's forces will eventually raid this place, and either arrest us, or worse, kill us."
A Yiga footsoldier looked at Master Kogha's corpse. "But what shall we do with Master Kohga's body?"
"He must have a will, right? Let's see what he wrote in it."
Mistress Karai and a few Yiga clan members searched the entire hideout for two hours, but they had found nothing. Perhaps Link stole it, along with anything else that seemed to have disappeared. They returned to the arena where Link had fought against Master Kohga.
"He has no will. Therefore, we will bury his body here, and afterwards, we will leave."
"For where?" the messenger asked.
The new Yiga clan leader sighed. "I don't know, but there's no time to waste. Now start digging!"
Three Yiga clan members started digging rapidly. Within less than 30 minutes, they had dug a hole deep enough and they lowered his casket into the ground.
"Master Kohga, you be forever remembered by your followers." the undertaker announced.
Karai took her sword and held it in both of her hands. "To my deceased predecessor, I will not rest until I find the man who did this to you. If Link is not vanquished by the time I find him, I will painfully destroy him." She sheathed her sword.
"Let Calamity Ganon guide you." the Yiga clan members stated in unison.
Mistress Karai stood next to Master Kohga's grave. "Now, we must go. Everyone follow me."
She marched forward, going through the Yiga clan hideout and leaving through the entrance. They climbed up a cliffslide to the top, and since the sun was setting, they could see Gerudo Town in the distance. Even further in the distance, they saw the Divine Beast, Vah Naboris, kneeling down for some odd reason. Karai shrugged it off and turned to address the group.
"Link could be anywhere by now. We must spread out our forces to find him. Lieutenant Oroku, take 20 soldiers and go towards the Necluda. Spread out your forces so that they can find him faster. Be sure to send two soldiers to the Hebra Mountains. I will take the remaining soldiers to the Akkala region."
Lieutenant Oroku took his troop and left. Karai and her army made their way to the Akkala region, which had taken six days since they traveled by horse cart. Karai looked at her or rather- Master Kohga's Sheikah Slate. Since he had no children, and the position was hereditary, she was next in line since she was his niece. Her slate had a few shrines on it-places she would go to later to try and find Link.
"Now spread out and find him."
The messenger looked at her. "What are you doing to do?"
"Using my uncle's Sheikah Slate, I will travel around Hyrule faster than most people and hunt him down myself."
"Master Kohga is your uncle?"
She sighed. "I prefer not to mention it, but... it is true. This matter of defeating Link is not only a pledge to Calamity Ganon. It's personal."
She put on her Yiga clan mask, got out the Sheikah Slate and teleported to the nearest shrine. Many weeks later, after the downfall of Calamity Ganon, Karai found her target; he had been at the entrance to Hyrule Castle. They were dueling in the courtyard, with Zelda watching from a safe distance. Karai fired arrows at him from afar, only for him to be stopped by his traveler's shield. He fired arrows at her in retaliation and they hit her mask, causing it to fall off. Link gasped.
"Who... who are you?" Zelda asked.
The Yiga Clan leader smirked. "The name's Karai, and you, Link, will pay with your life for the damage you've caused!"
He got out a boomerang, hitting it right in her head. She was knocked back. She quickly got up. The boomerang was caught by Karai the second time. Seeing how it was made out of wood, she snapped it in half with her knee. He got out a soldier's broadsword and ran towards her, only to be knocked to the ground. His sword slipped out of his hand and shattered. She had her right foot on his back, pinning him to the ground. She got out her eightfold blade.
"You will pay for what you've done!"
She was about to stab the sword into his back. "Karai," Zelda said to her. Karai looked over towards the princess. "Calamity Ganon has been defeated. You and your soldiers are fighting for nothing anymore."
"Maybe the others aren't fighting for anything, but this matter is personal." the Yiga clan mistress retorted.
Zelda looked at her, almost hesitant to speak. "What... what did he do? Maybe you can forgive him."
"He killed my uncle. For this, I'll never forgive him!"
Link was surprised, but he did not gasp. Instead he kicked her down and got off the ground. He got out the Master Sword as Karai stood up. She got out her vicious sickle and demon carver. Karai charged towards him, continuing to fight for revenge.