Note: This came from the one thing that I couldn't explain about EoE: why was Asuka lying next to Shinji on the beach?
Many people take "Asuka's" final words (kimochii warui loosely translated to "I feel sick.") to be figurative.
What if they weren't?

Shinji no Onegai (Shinji's Wish)
By DarkEnigma

Shinji gradually drifted to consciousness to the gentle sound of the ebb and flow of the sea. He turned his head to
the side as he lay on the soft sandy shore and took in the vision before him. The sea was red and reeked of blood.
He knew that it housed all the souls of humanity mingling together without AT fields to hinder them, though they could
return if they so chose. That was his wish. Despite his desperate loneliness, he did not want humanity to lose its
most essential human quality: individuality. He believed that DeCarte* used 'I' instead of 'We' for a reason.
Suddenly he saw a fleeting vision of Rei. A ghost of a smile flit across his face as he remembered the time he shared
with her when he was joined with Lillith. He had bared his soul to her and she had guided him to his final choice.
She and Kaworu where the only ones who truly loved him for him, besides perhaps his mother who now drifted among the stars.
Shinji slowly rose from the ground and noticed the body lying beside him on the beach. It was her. He grimaced
at the unwanted memories that surfaced of his final realization that she would always deny him. He'd been smitten with
her once: her pride, her confidence, her vitality, and her beauty. Yet in his time of most desperate need she would not,
could not accept him. Anger consumed him. He watched in horror as his hands unconsciously reached for her neck as they
had in his dream. He clutched her throat with singular purpose… until… until she gently caressed his cheek. He
immediately ceased his action and stared as her. He realized what he had tried to do and began to sob.
Her eyes opened. She saw Shinji sobbing over her and a wave of nausea came over her.

"I feel sick."

Shinji watched as she sat up and stared into his eyes. Suddenly, her face broke into a smile.

"There is no need for you to cry, Ikari-kun."

She watched his eye open in shock.

"A-a-a-asuka?"

"No. I am she that loved you in the body that you lusted for. Sohryu could never accept you but I always will."

He gasped, "Rei?!"

"Hai. This is part of your wish Ikari-kun. You did not want to be lonely anymore."

She slowly embraced him. He was trembling terribly so she turned to face him a placed a soft gentle kiss on his
lips. Shinji's tumultuous mind ground to a halt. This was right. This was good. He was happy, perhaps for the first time.
He returned her embrace and her kiss tenfold.

*DeCarte coined the phrase "I think, therefore I am."