Link was forced to act too soon.
He felt the same despair Ganondorf's magic brought begin to settle in the room. The hero knew it came from the Sacred Realm. With it nearly overwhelming him, the seal must have been close to failing.
Link spent several minutes cleverly leading Dora around the temple. He would have been a fool to believe she was not aware of his trick. It was when he parried her attack, and instead of following through darted for the door, that she countered his strategy. She fired the loaded bolt from her crossbow. Link realized the sound of her boots chasing him down was absent, and spun around to see what fate awaited him. That was when he was caught in the right bicep by the bolt speeding toward him. He cried out in pain, even dropped his shield, and seethed at the sting. It was a new agony he never experienced.
He immediately recalled his training, and determined if the arrowhead only pierced him, or impaled him. He found the point of the bolt stuck out the front of his arm. In this case, he could potentially break the arrow and just remove it, but he would need to staunch the flow of blood. There was no time for any of that, because Dora was about to kill him.
She was wise enough to not come in from above and leave her entire torso defenseless for this attack. Nor did she jump high into the air as she might have with some previous opponents. Her crossbow hung freely at her side again, and she sprinted in for the kill faster than Link could react. Her sword was across her body, poised over her shoulder. When she reached him, she unleashed her arm to tear open his torso with her blade, and prepared to follow through with a swift spin to bring her heel into his face.
Except, her sword's lust for the hero's blood never had the chance to be sated.
Link gritted his teeth against the pain and tightened his grip on his shield. Dora's sword bounced against it and vibrated. She never expected to miss, and the force knocked her off balance. He stepped forward with one long stride and sliced her sword arm as she held it out, exposed, to stay on her feet.
Ganondorf spun at the sound of her scream. His terrible eyes glared viciously, as if he dared the hero to strike again.
The agony of the pure blade infecting Dora's body crippled her. Her sight was filled with the white of the searing pain, and she never knew Link aimed to pierce her until the blade was already imbedded in her stomach.
Dora refused to lose her precious sword. Instead, she gripped it tighter as she collapsed to her knees with the Master Sword protruding from her torso. She cursed herself for allowing him to surprise her like that.
Something happened after that. She did not continue to fall onto her side, or experience the bitter cold of the stone floor, or even land face first in one of the salty puddles. There was warmth surrounding her, supporting her. When her vision cleared, she looked up into Ganondorf's handsome yellow eyes. He knelt and slowly eased her down with him where she could rest. Her face contorted and she cried out as the energy to fight evil coursed through her body. Having him close made the pain severe, but she did not care. If she was going to survive, she needed his help. If she was going to die, there was no one else she wanted at her side for the last moments.
Ganondorf grazed his hand over her abdomen and inspected the wound. The skin around the entrance was pale. Already she lost so much strength. His power could not heal her. It would only inflict more damage. Blood poured uncontrollably out of the opening in her stomach. Dora gripped his shoulder tightly as the waves of pure energy rushed over her and stole her breath. He did his best to keep a face of stone, but she read her imminent death in his eyes.
"I am sorry I could not protect you to the end," she whispered in a trembling voice.
Ganondorf shook his head slowly. The pain she suffered, all he wanted to do was take it from her. He could endure it better than her. "You have done exactly what you were meant to do. You made this victory possible." He squeezed her dominant hand that gripped the sword, and encouraged her to release it.
"This is a first, at least, that my death precedes your own." She managed a weak laugh, as she used all her strength to uncurl her fingers from around the hilt of her precious wedding gift. "Use it to avenge me, my king."
He gently lowered her closer to the floor, with her sword secure in one hand, and the other hand curled around the back of her neck to support her head with his fingers. "It will be glorious."
Her eyes became wide as shock set in from the loss of blood and the convulsions that overwhelmed her muscles. As much as Ganondorf knew he would see her again soon, he never eliminated the possibility that he might not. He wrapped his arm fully around her back and held her tight to his torso. He whispered those three little words for only her to hear, that only she earned.
Through the pains of her failing heart and mind, she smiled. "I love you too," she breathed and kissed him one last time on the cheek. His comforting embrace reassured her that she would unite with him soon and she accepted death.
He felt her body's strength vanish, and where she should have been heavier, she seemed lighter. Never before had she been like an angel than in that moment. He rested her head against the floor and closed her eyes with his fingers. The ache in his chest caused by the loss of his wife at his enemy's hand was unfamiliar and strange. There was only one way to fill that void.
Ganondorf could not accept failure, for Dora's sake. He stood tall and proud, with his wife's corpse at his feet, and faced Link. He turned this strange sensation of grief into loathing and hate, until his entire body glowed with an evil aura that overflowed from him like flames. "I will make you regret ever being born, boy!" he shouted in a dominant, bold voice, that echoed between the walls of the temple.