"The ends justifies the means," even if it means abandoning your only child. But what, just maybe, in a different time, a different place, an alternate universe, if you will, it actually means -raising- that child.

Maybe things will go something like this...

Neon Genesis Evangelion is owned by Gainax
-------------------------------------------

Shinji ran, the monster's terrifying roar reverberating in his ears.  Tears of shame and fear streamed down as his face, blurring his vision.  "Mommy," he mumbled, tripping and falling on the cold hard floor. He quickly stood up, and for a few moments, his tears ceased.  He spotted an open door and quickly ran towards it.  He entered a room and started whimpering once more.
The room was empty, there was nothing there to protect him; but the room was dark.  The darkness might help him, he knew.  He ran to the far wall and sat down against it, hugging his knees to his body.  He closed his eyes and stopped crying.  "Mommy," he repeated softly. (Please be okay, please be okay, please be okay,) he thought in silent prayer.

Several hours past as the child kept his fearful, silent vigil; then he heard footsteps come towards him as the clicking of a pair of boots grew louder and louder.  "Shinji," a voice said, silent and commanding.

Shinji opened his eyes and looked up, the fear leaving him in droves.  "Daddy?" he queried hopefully.  The man knelt down in front of Shinji and gently put his hands on the boy's shoulders.  "Is Mommy okay?" Shinji asked.

"Shinji.  Your mother. . . is gone," the man replied.

"Gone?" Shinji asked in a small voice.

"Yes.  It's your fault.  You ran away, Shinji.  You weren't there to protect her, so she was taken away."

"My fault. . ," Shinji repeated, his face burning with shame and self-loathing.
"I'm s-sorry, Daddy!  Please bring Mommy back!  Please!  I'll do anything!  Just bring her back!" the child wailed.

"Really, Shinji?  Will you really do anything for your mother?"

Shinji wiped away his tears, looked up at his father and with love and trust in his eyes, and nodded.  "Excellent," Gendo Ikari replied, gently embracing his son, a small, calculating grin growing on his face.


His Only Begotten Son
----------------------
By: Anand Rao


Chapter 1:  Born in Darkness
------------------------------

10 years later....
-------------------


Travel bag in hand, Shinji walked to a nearby telephone booth that was located just outside the airport.  He walked inside the booth, picked up the phone and dialed NERV Headquarters.   After two rings, the line picked up and a pleasant female voice said, "Please state your name and access code."

"Shinji Ikari, access code 8697923-Delta E," he replied.

"Thank you, Commander. How may I direct your call?"

"Transfer me to Commander Ikari," Shinji requested.

"Yes sir, one moment."

A few seconds later, the call was transferred and Gendo Ikari picked up the phone.  "Ikari here," he answered.

"Hello, Father," Shinji said.

"Where are you?"

"Standing outside of Tokyo-3 Airport," Shinji replied.

"You're early," Gendo observed.

"Yes.  I heard about the accident, and decided to return a few days ahead of schedule.  Besides, I needed to get away from that red headed sow," Shinji explained.

"I'll send someone to pick you up."

"Thanks.  Bye," Shinji replied, hanging up the phone.  He exited the phone booth and stared pensively at the bright blue sky.  (Soon, Mother.  It will all start soon.)


            **************************************

"Hi, Shinji-kuuun!  Welcome back!"

(Oh God, why did he send her of all people?) Shinji silently groaned.  A blue, two-door coupe sped towards him, the driver, a buxom and rather attractive woman, stuck her head out the window and waved at him.  For a few seconds, the car seemed to accelerate, then came to a sudden, screeching halt right in front of him.  If he was worried or scared at all, he gave no sign of it as he politely smiled at the driver.  "Hello, Captain," he said.

"Come on, Shinji-kun!  You haven't been gone that long, it's Misato, remember?" the drive chided him.

"Misato," Shinji conceded.

Misato stepped out of the car and rushed towards him, nearly tackling him in a tight hug.  "I've missed you, kiddo.  How was Germany?" she asked, fondly mussing his hair as she released him.

"Germany was fine.  Shall we get going?" Shinji asked, walked towards the car's passenger side.

"Sure," Misato replied, her smile faltering.

After they had been seated and properly belted in, Misato stared the car, and drove towards NERV headquarters.  The pair sat in silence for a few minutes before Misato decided to strike up a conversation once again.  "So, did you get along well with Asuka?" she asked.

"Well enough."

"I see," Misato floundered, trying to figure out how to keep the conversation alive.  (I'll break that wall around you, Shinji.  Just watch!) she thought determinedly.  "I read the reports on her synch scores.  She's catching up to you.  In a couple more months, she might even be a match for you, First Child," she said teasingly.

"Perhaps," Shinji replied, forcing himself not to let out a sigh.  (Doesn't she ever shut up?)

"Not that I mind, but why did you cut your trip short?  Did your father call you back?" Misato asked.

"I heard about the accident."

"I see.  You came back for Rei," Misato realized.

Shinji clenched his right hand tightly, the only sign of his growing irritation.  Realizing that perhaps she had gone too far, Misato remained quiet for the remainder of the trip.


            **********************************

Upon reaching headquarters, Shinji headed directly to his father's office.  As was his habit, he knocked three times in quick succession on the front door, then opened it.  He entered the office and saw his father sitting at his desk, studying a report from the Marduk Institute.  Looking at the classified folder, Shinji had to admit, his father carried secrets as far as they could go.  He stood silently in front his father's desk and waited.  "Was it recovered?" Gendo finally asked, still reading the report.

"Yes, Kaji should be bringing it here in a few weeks," Shinji replied.

"We have been unable to locate the Fourth," Gendo commented, placing the report on his desk.

"Is the Fourth already necessary?" Shinji asked.

"If the reactivation test of Unit 00 fails again, then most likely."

"How's Rei?" Shinji asked.  Before Gendo could answer, the door to the office opened, and a woman with short blonde hair, wearing a long white lab coat entered.  Shinji stiffened when he saw her, but remained silent.

"Shinji, welcome back," she greeted hesitantly.

"Dr. Akagi," Shinji replied coolly.

"Our final analysis of Unit 00's reactivation procedures have been completed.  We'll be ready whenever Rei is," Dr Akagi said, turning towards Gendo.

"Thank you, that will be all," Gendo replied, dismissing her.

"Yes, Sir," she replied.  She glanced at Shinji once more before exiting the office.

"Is there a problem?" Gendo asked mildly after Ritsuko had left.

"Nothing I haven't brought up before," Shinji replied.

"You're letting your personal feelings cloud your judgment.  I'd have thought that you would have outgrown that by now," Gendo observed.

"We can't trust her, Father.  You said it yourself, she's just like her mother!" Shinji snapped.

"You find someone else who knows as much about the Magi as she does, and I'll replace her," Gendo offered.

Shinji sighed and closed his eyes for a few moments.  "Do you enjoy fucking her?" he finally asked.

"It keeps her in line," Gendo replied.

"You're one cold hearted bastard, Father."  Shinji turned away from Gendo's desk and walked to the door.  "I'm going to go see Rei," he said.

"You're right about me, Shinji, but are you any different?" Gendo asked, his tone slightly amused.

Shinji stopped, then shook his head slightly. "Of course not, Father.  Only cold hearted bastards like us will survive in this new world you're creating," he replied.

            **************************************

Shinji opened the door to Rei's hospital room and stepped inside.  He stopped there, at the doorway, and looked at the pale blue-haired girl who was lying in the room's single bed.  A thin white sheet covered her legs and torso and there were thick bandages wrapped around her arm, neck, and head.  A cold rage built up within him as he slowly walked towards the bed.  (That bitch must have been responsible for this!  She hates Rei, I know it!) Shinji thought.  Noticing that Rei was awake, Shinji ventured a weak smile.  "Hello, Rei," he said.

Rei's uninjured eye turned towards Shinji.  "Ikari-kun.  You're back," she replied.

"Yes.  I heard about the accident," Shinji explained.

"Commander Ikari saved me."

"Yes.  I. . . I know.  I'm glad that you're okay."  Shinji gently grasped hold of Rei's hand and squeezed it tightly.  "I don't know what I would do if I lost you," he admitted.

"You won't lose me, Ikari-kun," Rei replied.

Shinji's smile widened and a look of relief crossed his face.  He heard the door handle click, and he suddenly pulled his hand from Rei's grasp.  He door opened slightly and Misato poked her head into the room.  "So, how's the patient?" she asked brightly.

"Recovering," Shinji replied coldly.

"Great!  I thought I'd find you here," Misato said, opening the door completely and entering the room.  "Hello Rei, how are you feeling today?"

"What are you doing here?" Shinji asked; it was almost an accusation.

"You're not the only one who worries about her, Shinji," Misato rebuked, a bit offended at Shinji's tone of voice.

"I have to go," Shinji said abruptly.  He stepped back away from the bed when Rei quickly grabbed his hand.  Her face contorted in pain for the effort, and Shinji sighed.  "I guess I can stay for a few more minutes," he said uncomfortably.  Rei released his hand and sank back into her bed.  Misato hid a smile behind her hand and coughed amusedly.  "Is something wrong, Captain?" Shinji asked pointedly.

"Not at all," she replied easily.  "It's good to see you're recovering, Rei-chan.  I'll leave you two lovebirds alone now."  Misato smirked teasingly at Shinji then walked out of the room.

"God, I hate her," Shinji growled.

"Why?"

"Huh?" Shinji asked, looking down at Rei.

"Why do you hate her?" Rei asked.

"Because. . . because she won't leave me alone!  She always wants to know what I'm doing, or what I'm feeling.  She can't mind her own business," Shinji replied.

"She cares for you," Rei observed.

"Not really.  She just wants to use me.  No one here cares about anyone, Rei."  Shinji stepped back away from the bed again and turned towards the door.  "I really do need to get going, but I'll see you again in the evening, okay?"  Without waiting for a reply, Shinji left the hospital room.


            *****************************************

"Father," Shinji said, swallowing the piece of steak he had been chewing, "after Rei gets out of the hospital, why don't we move her in with us?"

"That would be unwise," Gendo replied, cutting into the thick slice of meat in front of him.

"It would only be temporary," Shinji said quickly, "until she fully recovers."

"I warned you about getting too attached to her, Shinji.  Never forget what she is, or what her purpose is," Gendo replied.

"Yeah, and I'm sure those burns are on your hands because you hate her," Shinji snapped back sarcastically.  Gendo carefully set his fork and steak knife on his plate and stared neutrally at his son.

"Shinji, when I first decided to involve you with NERV, I was worried that it might be a mistake.  I was just going to dump you somewhere, because I didn't have the time to coddle you or raise you; I still don't.  I brought you into this because you are the only person who would want this to work as much as I do.  Don't make me regret that decision."

Shinji sat in red-faced silence and continued to eat his dinner.  (Why can't I love her?  Just for a little while?) he thought.  "I'm going to go catch up on the homework I missed."  Shinji stood up from the dinner table and walked towards the stairway that led to his upstairs bedroom.

"Shinji."

"Yes, Father?" Shinji stopped half way up the stairway and turned towards the still seated Commander of NERV.

"We're very close to realizing our goals.  Don't fail me again, now."

"Y-Yes sir."  Shinji turned away from his father and ran upstairs to his room. He quickly entered his room, locking the door behind him.  (Damn!  After all this time, I'm still scared of him,) he thought bitterly.  He turned on the light and climbed into bed.  (Just wait until Mother's back, then you'll see, Father.  You don't know her.  You don't know her at all.)  He stared at the ceiling for a few moments, his eyes slowly losing focus; then suddenly, he was asleep, and in sleep, he remembered...


"You want -me- to get into that monster?"  Shinji demanded, staring at his father in shock and fear.

"Yes.  In the years to come, you will pilot Unit 01.  You will learn start learning that process now.  This is important, Shinji.  Don't run away again," Gendo replied flatly.

"But. . . but. . . Father, I- I. . ."

"You said you'd do anything, Shinji.  Remember?"

"Yeah, but, that- that..."

"Do you want to save her?  Or are you going to run away, again?"  Gendo asked quietly.

"All right.  I- I'll do it," the boy guiltily agreed.

"You'll need to wear this," Gendo said, handing Shinji a plug suit.  "Go into the dressing room, get changed and come back here."

Not trusting himself to reply, Shinji grabbed the nylon suit and ran to the dressing room.  Once safely inside, he began to shiver uncontrollably.

"I won't run away, I won't run away, I won't run away," he repeated to himself.  That purple. . . monster had taken his mother, and now it was coming for him.  He wouldn't run away; not this time.

He promised his father.

He promised his mother.

Still shaking slightly, Shinji donned the plug suit and walked out of the dressing room.  "I'm ready, Father."  Shinji announced, walking back to where Gendo was standing.

"Good.  Take the catwalk to Unit 01's cage, Dr. Akagi is waiting for you there."

"Does it have to be her?" Shinji asked plaintively.

"Shinji, just go."  The expression on Gendo's face brook no argument, and Shinji walked hurriedly toward's Unit 01.  Ritsuko helped him get comfortably seated in a large white tube which would serve as the Eva's entry plug.

"There's really nothing to worry about Shinji," Ritsuko tried to assure the young boy.  "All you need to do is sit back and relax, okay?" The blonde doctor's weak smile was the last thing he saw as the cover of the plug closed shut.   For a few moments, Shinji stared breathing heavily, willing himself not to scream.

The plug's internal lights turned on, and Shinji felt himself spiral downward as the plug was inserted into Unit 01.  "Hey handsome!  Ready to make history?" Misato's all too cheerful voice asked over the entry plug's internal speakers.

"Er, I guess so," Shinji replied. The plug suit gripped his body tightly, and he could already feel himself sweating all over.

"Great!  We're almost ready to get started, to just sit back and relax, okay?"

"Okay."  Shinji nervously tapped his foot, hoping that whatever test his father was performing would be over soon.  Hearing a light splashing sound, Shinji looked down with alarm as water quickly filled the entry plug.  "Um, I think there's a leak in here somewhere," he blurted.

"That's just the LCL, Shinji," Misato explained.

"Oh yeah."  Shinji blushed, vaguely remembering what Ritsuko had told him about the breathable liquid that was quickly rising all around him.  As it rose above his chest, his breathing quickened, near the point of hyperventilation.

"Shinji!  Calm down!" Ritsuko ordered.  "You're not going to drown."

As the LCL rose above his chin, he closed his mouth and held his breath.  (She's going to kill me!  Mommy!  She's trying to kill me!) Shinji mentally screamed.  After a few more seconds, his mouth burst open, and the LCL filled his throat and lungs.  Reflexively, he swallowed it down, feeling it hit his stomach like a rock.  He gagged as the oxygenated liquid moved freely through his nose and mouth.

"See?  That wasn't so bad, was it?" Misato rhetorically asked.

(Bitch,) Shinij thought, glaring bitterly at the controls in front of him.

"It will just be for a few moments, Shinji, then you can get out," Ritsuko said.

"Right," he replied.  Shinji leaned back in the seat and closed his eyes.  (Mommy, where are you?) Shinji sighed, trying to sink deeper into his seat.  He would wonder later if he had been dreaming or hallucinating, but the visions came, and he would remember them in crystal clear clarity.

He felt a gentle touch, a loving caress, and Shinji opened his eyes as a white, willowy shadow embraced his body.  He felt warm, and safe; safer than he had in years.  "Mommy," he murmured softly.

* Shinji. *

"Mommy, is it that you?"

*My son. *

"Mommy. . .I - I'm sorry! I was scared!" Shinji wailed.

*I will protect you.  Now, and always.*

"C-can you come back home now?"  Much to Shinji's alarm, the white shadow started to fade away.  "No!  Come back, please!"

*You will learn, Shinji, when you're older, that life is lived in the present; not the past.*  The shadow faded completely and a few seconds later, Shinji heard Misato's voice congratulate him on what a 'great job' he did.  He had no idea what so ever what she was talking about, and at the time, he really didn't care.  His mother would protect him; she was on his side, and that was all that mattered...

Shinji opened his eyes and rose from his bed.  He stared at the stack of papers that was sitting on his desk.  "Well, I'd better at least give the -impression- that I care about school," he muttered.

*********************************

The End: Chapter 1

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