What had she been thinking?

Zelda, for having grown up in a castle, was a wordlier person than most people assumed. She had escaped Ganondorf's clutches as a child, grew up on the run, and helped to guide the Hero of Time on his journey from temple to temple, under the guise of a Sheika man. Zelda cared too much for Link to not give him every bit of help she could, without allowing the Evil King to locate her.
Which is what brought the princess here, to the Water Temple… alone. It'd been days since she had watched Link enter, and hadn't seen him since. So, against her better judgment, she followed him in.
It wasn't much effort to make it as far she had. Most enemies could be evaded, and the puzzles that now plagued the Temple were difficult but not impossible. She was safe in the knowledge that Link had made it, and that he was ahead of her, because there were no maps, no compasses, nothing that could have helped her make it to the last room of the Temple any easier. On the plus side, she hadn't found his corpse anywhere, so that was something to be thankful for.
Finally, she would come upon a more peculiar room than the others. The room was seemingly endless, with a shallow pool of water that stretched on as far as the eye could see, with a just as expansive sky of blue. She took a step forward, and seemed to float on the very water on which she stood. The disguised princess made her way to a small plot of sand, with a tree in the center. On the tree was a nasty bit of blood, and she prayed to the Goddesses it wasn't Link's. Her last thought was, how peculiar it was that there should be no foe in here…

By the time she knew what had happened, she was on the ground, pinned, with a throbbing head. Zelda opened her eyes, and, kneeling on her chest was the very man she had been looking for!

Or… Was it?

Link let out a rough, deep laugh, and immediately Zelda knew that was not the hero she'd been seeking.
"Well, well, well, what have we got here?"
He seemed to look like Link, but any real traits of his were obscured by his shadow-like appearances. Where Link's blue eyes would have been, were red ones. Where his kind smile would be, was something much more sinister. His voice was rough and jagged. Soulless, even.
"Unhand me!" With her free hand, she quickly summoned a knife, aiming for the entity's forehead. In just as quick a movement, his sword was out, up, and plunged into her palm. She grit her teeth, refusing to let anything but a forced whimper escape her lips.
The imposter watched with shock and awe as she transformed beneath him. Maintaining her form was a matter of concentration, and the sword in her hand saw to it she had none. Below him she regained her true form, of the Princess of Hyrule.
His eyes darted over her body, and Zelda searched them eagerly, desperate to know her fate. He was heavy and strong; she could not push him off, nor weasel her way from under him with his sword in her hand and his knees on her chest. The shadowy, dark Link grinned and she felt a chill run up her spine.
"Princess…" He breathed, regaining composure. "His Princess."
"Where is Link?!" Zelda wouldn't give him the pleasure of scaring her. "I saw blood, is it is?! Unhand me, beast!"
The shadow Link laughed, but he did not get off of her. "You have greater concerns at the moment."
Zelda hadn't considered this. She knew she would encounter beasts, monsters and maybe some crooks along the way, but the way his eyes ravished her body, and his heavy weight baring upon her… She became aware of an entirely different kind of fear. In an instant she kicked her legs up, just to be hit in the face with his fist in return.
He hit her again, and again, and again. With his hand off hers, it freed her to she reach forward and grasp for his throat. The shadow Link lept from her grasp, pulled his sword along with him, and along with it, the innards of Zelda's hand. She gasped in pain and sat up, scooting back, turning over and crawling… anything to get distance from him. Before she could stand, before she could run, he was upon her again, beating her head into the surface water beneath them. The pain wasn't so bad, but she could feel herself begin lose consciousness. She tried to push herself up and away, but he had her pinned. By the time he stopped thrusting her head into the ground, she was too weak to lift it back herself. How could she have been so careless, waltzing into the room with nary a concern?
As the princess fought to keep conscious, she heard the tearing of cloth behind her. The imposter had ripped her skirt.
With the last vestiges of her strength, she screamed and threw her head back, nailing the front of his head with the back of hers. He grunted angrily, more annoyed than anything. With one hand, held her head down in place. She squirmed beneath him.

This could not be happening.

She felt his hand rip the back of her tights, and her undergarments off with one foul swoop. Her skirt was hiked up to her waist. She was as bare below the waist as the day she was born. Refusing to surrender, she finally swallowed her pride and screamed out. If Link was near, he'd hear it; If he didn't, maybe she'd get lucky and a monster would. A less evil one.
The shadow Link chuckled. He could feel his breath on her ear as he nestled in above her. Zelda felt a warm sensation on her most private of areas, and cried out in sheer panic.
But she still couldn't move. His head locking her down and one of her hands completely incapacitated… The princess tried to steel herself for what would come next. She was barely present for it.
The thrust was hard, and she tore. She closed her eyes and imagined the blood leaking from within her. He grunted in pleasure, right next to her ear. Zelda turned her eyes to the ground, refusing to look at him.
"I bet this is your first time." He breathed into her ear. "So tight, like a good little girl."
His breath was hot on her neck, as he thrust over, and over, and over again, each one bringing a new wave of pain and dissonance from her body. The monster clutched onto her shoulder in the throes of pleasure. His weight crushed her. He reached under her dress and clawed at her breasts. He bit her neck. She likened herself to a doll, made solely for the shadow's taking. Before she entered this room a princess; she would leave it a chattel. His fingers pinched at her nipples and she cried out in shock.
"Like that, did you? My sweet little harlot."
He grunted, and groaned, and carried on like the beast he was until he finally, with one final, gut-wrenching thrust, was finished. She felt his warm essence inside her. Zelda closed her eyes, and allowed a single tear to escape her eye. The world fell away.

When the princess awoke sometime later, he was gone. She was left in a small pool of fluids.. Some hers, some his.
Zelda moved, with purpose; she had to get out of the Temple. She had to find Link. She had to heal her hand. She had to help save Hyrule.
The princess told herself she would not speak of this – nor think of it – again.

Oh, what had she been thinking?