Ayanami Rei was dead. Her body had burnt up in the explosion of Unit 00 while trying to defend the Earth from an Angel Attack. Her mourning was short, and NERV, having felt as though they were now done with their doll, moved on with their ordinary lives. They had no reason to feel remorse; they still had two other pilots to do their bidding.
"Do you think we lost something special in Rei, commander?"
"No, Fuyutsuki. She was a mechanical pilot, capable of following orders, and nothing more."
"The other two are different?"
"If you buy two pigs, they will compete for food and become fatter in time for harvest than if you bought only one."
"I see. And Rei was incapable of competition?"
"She didn't see the point. She wasn't made to see it."
"Right…"
Defeating the Angel that Rei had failed to neutralize was quite a feat, and all of NERV's personnel had gathered to celebrate. Shinji and Asuka, tired and injured from the fight, convalesced in a public hospital, and thus were not present to behold this spectacle.
The commander had spared no expense for this celebration: All NERV employees regardless of specialty were given the rest of their day off, during which time any of a variety of food and drink would be provided to them. Commander Ikari, confident that there would be only a few Angels left, felt safe in giving every NERV officer a substantial pay raise, and an equal celebration.
The very top of the chain of command; namely Commander Ikari, Fuyutsuki, Misato, Ritsuko, Maya, Shigeru and Makoto, were celebrating in the command bridge, when an unwelcome visitor made entrance into their festivities.
The room fell silent as the automatic door to the bridge closed, and a single dire figure walked steadily forward. From his high seat, Commander Ikari could just make out the silhouette. "Who is that down there?" Makoto called back from his position, saying in shock, "It's…It's Rei, Commander."
Commander Ikari stood up, and took an elevator down to the level where the figure had intruded. He emerged, and beheld with his own eyes that this figure was in fact Ayanami Rei, the late pilot of Evangelion Unit 00. He started to speak, but seemed for once to be at a loss for words.
"Rei… I… How?"
She simply turned away and ran back the way she had come. Commander Ikari gave chase, disregarding his usual reserved mode due to shock and awe. The agile girl easily outran the Commander, who tried as he could to keep up. Rei sprinted through the Evangelion Cage walkway, the Medical Facility, and the Corporate Offices of NERV HQ before veering right, through a large metal door. The Commander followed, finding himself in an advanced state of darkness, so dark that it seemed to give pressure on his chest, making breathing itself an arduous task. He groped around in the darkness for anything to latch on to, but found nothing. As he floundered about, a quiet voice caught his attention.
"I heard what you said, Commander."
"Rei?"
"That I was only capable of following orders. Did you order me to do this?"
"Of course not, Rei! I…"
"You lost a valuable doll when you lost me, Commander."
"You aren't a doll to me, Rei. You're-"
"A plaything? Something on which to take out your rage and lust?" A light flickered on, and the Commander found himself in the stark medical room where Rei was created. She stood next to a hospital bed, wearing what remained of her plugsuit.
"A shadow of your wife, who you lost trying to play God?"
"Rei…" The Commander's rage grew, and he reached down, drawing a small pistol from his pocket. "Don't make me do this, Rei…"
The NERV personnel who had followed their Commander ran quickly to his aid when they heard a gunshot sound, followed by a male voice crying out in pain. They entered the stark medical facility, and found the Commander on the floor, the mask of death across his face, as Rei stood over his body, arms out to receive them. As they approached to restrain the pilot, they dropped one by one, all realizing the trueness of death that Ayanami Rei had never experienced.
"You should not have forgotten me. Who now is truly heartless?"
Ayanami Rei awoke suddenly in her apartment. A small clock on the opposite wall read 0230, illuminated by bright moonlight flowing in from the window. Re went back to sleep, until it was time for her to rise and do her duty once again.