Final Understanding
Final Understanding

Shinji Ikari sat on his bed with his hands in his lap.

"It's over…finally." It had been a week since the final Angel had been defeated- a week since he'd piloted his Eva; a week since he'd felt useful.  Right now, his position at NERV was uncertain.  His father still held his position, but then again, he and his father had never communicated.

"Hmm…I wonder what everyone else is doing." Feeling rather bored, Shinji stood up from his bed and went to go see if anyone else was home yet.

Upon walking out of his room, Shinji saw a familiar figure walking into the kitchen.  Her long mane of fiery, red hair flapped behind her, and he followed after her.

Asuka cracked open the fridge to see if there was anything decent to eat.  She managed to find a microwave dinner that was still sealed and yanked it away from Pen-Pen before he saw it.

"Asuka?" The German pilot almost jumped to the ceiling, and she turned around to glare at a helpless Shinji.

"Dammit baka, you scared me half to death!"

"S-sorry about that," he said sheepishly.

"What do you want?" Shinji blushed slightly.

"Well…um…I was just wondering if you were feeling any better." Asuka's eyebrows quirked up.

"What do you mean…better?"

"Misato told me that you weren't able to fight during the battle with Kaoru, and I was just wondering if you were doing any better." Asuka had to hide the smile that wanted to appear on her lips; she felt something tug at her heart as she heard the concern in his voice.  He'd actually been worried about her.

"What's wrong, baka, can't handle your own?" she teased. "Not that's it any of your business, but I'm perfectly fine!" Asuka knew that she was lying, but the last person that she wanted to be weak in front of was Shinji Ikari.

"Oh okay, I was just curious.  By the way, I was going to go see if Rei was doing any better.  Would you like to come?"

"Why would I want to go see wondergirl?" Asuka said with a slight amount of venom in her voice.

"I…I don't know.  I was heading over there and just thought I'd ask." Asuka smirked at him.

"No thanks, but tell your 'girlfriend' hi!"

"She's not my girlfriend!" Shinji almost shouted.  Asuka burst out laughing.

"Oh…did I strike a nerve, little boy.  Why are you so concerned about her?  Do you love her or something?" Shinji didn't answer right away, and Asuka felt a pang of jealousy swirl through her.

"During the battle with the fifteenth Angel, Rei risked her life to save mine, and I thought she was dead.  But now that I know that she isn't, I want to repay her for her kindness." Shinji's voice held a strange determination, and Asuka's eyes widened slightly.  Her stomach growled, and the rest of her thoughts faded away.

"Enough talking, I'm starved.  So unless you're volunteering to cook for me, get out!" Shinji hastily retreated before Asuka hit full burn.  He headed out through the living room and let out a much-needed breath.

A smile crossed his face.  He was glad that Asuka was all right, and he was glad that Rei was going to be all right.  Suddenly, he asked himself why he felt such an odd feeling inside when he thought about them.  True, they were both his 'friends', but there was something more that he felt for them.  Were they like sisters…no, it was different… it was deeper than that…

The door to the apartment swished open and in walked Misato.

"Hey Shinji!"

"Hi Misato, I was just on my way out."

"Why…you got a date?" Misato couldn't resist teasing him, even though she knew that Shinji didn't have a girlfriend.  It was worth it to see him turn as red as a tomato.

"Misato, that's not funny!" he whined and quickly ran out the door.

Shinji walked down the endless sections of corridors to NERV headquarters, heading for Rei Ayanami's quarters.  He was just about there when the internal alarms went off.

"SECURITY BREACH ON LEVEL 12:  ALL STATIONS TO FULL ALERT!"

Level 12…that was the same level that his father's…the Commander's office was located on, but how would someone gain access to that.  Although, he nearly hated his father, Shinji decided to investigate.  He ran back down the hall and jumped back into the elevator.

Normally, someone would have to punch in several access codes just to gain access to Level 12.  Shinji was planning on getting off at Level 8 and asking to see his father.  However, all the safeguards had been disabled.

Shinji exited the elevator and gasped in shock.  All the security guards were dead, and the computer interfaces were smashed.  Now, he knew that something was seriously wrong.  Although he'd never been there before, Shinji knew the layout of this level and headed for his father's office.

Upon reaching Gendo's office, Shinji noticed that the double steel doors were forced open.  Squeezing through the dangled metal, Shinji froze in place.

"Don't move, Ikari!" It was Ritsuko, but she was holding a gun.  However, she wasn't pointing at him but at his father.

"Why commander?" The man just stood there with a blank expression on his face.

"Ritsuko?" Shinji spoke softly, and the blonde turned to glare at him.  Her eyes narrowed, and Shinji felt someone behind him.  Glancing back, his eyes came to rest on the form of one, Rei Ayanami.

"You!" Ritsuko growled and pulled a second weapon from her belt.  She aimed it towards Rei, but the young pilot didn't flinch.

"No Ritsuko, don't harm her!" It was Gendo's voice this time.

"Why commander…why did you pick her over me?" Ritsuko's eyes shot daggers at him, while unshed tears lay in their depths.

"Even when you make love to me, you still don't care.  What's so special about her?  Is it because you used your own wife's cells in her body?"

Shinji listened in complete silence.  He remembered seeing the clones that Ritsuko had shown him, and how she had destroyed the remaining ones in a jealous rage.

"Ritsuko, if it is me you want…" Rei walked by Shinji, and the irate woman trained a gun on her.

"Shut-up, you bitch, you're the cause of my problems.  He always cared more about you than anything else; you were his perfect creation- his perfect woman.  Now, I'll take what he cares about most."

"REI!" A shot rang out, and the pilot of Eva 00 calmly waited for the bullet to strike her.  She felt no impact and opened her eyes.  Shinji was standing in front of her, clutching his left arm, which was bleeding profusely.

"Why…why did you save her?" Ritsuko gasped and backed away.

"Because she's my friend, that's why.  But you wouldn't understand that!" Shinji spat at her.

"Well Commander…" Ritsuko turned back to look at him, "…like father like son, eh?  So tell me, you both screwing her or just Shinji?"

"Shut-up Ritsuko!" The younger Ikari hissed as he squeezed his hand around his wound.

"My...my…Ikari, so you do have a temper," Ritsuko laughed.

"Tell me, Ritsuko, who put you up to this?" Gendo asked. "Did SEELE put you up to this?  What'd they do…promise you my position if you got rid of me?"

While the Commander had her distracted, Rei was able to check on Shinji.  She tore off part of her uniform and wrapped it around his wound.

"Thanks Rei." She let a small smile creep up on her lips; it was one of the rare times that Shinji had seen her smile.

"No Ikari…Shinji…you risked your life to save mine." He grinned at her slightly.

"Well…you did the same for me, so we're even now."  Their attention was turned back to the two feuding adults.

"Actually Commander, they did promise me your spot, but I said that I'd rather just kill for the heck of it.  So tell me, any last words?" Gendo snorted and laughed at her.

"Yes.  You will never be as good as her; you will never be as good as Yui." Ritsuko became enraged and fired.

"You're a bad shot, Ritsuko," Gendo sneered as he held his hand against his abdomen.

"I missed on purpose." Ritsuko proceeded to unload her entire clip into the Commander's body.  She laughed sadistically when he collapsed to the floor.

"No!" Shinji and Rei said at the same time.

"Freeze!" It was the security patrol responding to the alarm.  Ritsuko laughed and aimed for them.

"My job is done." She fired one shot then was gunned down by the five security guards.

Shinji stumbled around the large desk to the prone figure on the floor.  The Commander's body was motionless, and the young boy knelt beside him.  Suddenly, the man's eyes opened, and his head turned towards the young Ikari.  Rei knelt down next to Shinji and gazed down at the man that had made her.

"You two have done well," the older man coughed as blood dripped from his mouth. "However, time is short, and there are several things that you must know."

"Please Commander, save your strength, the meds will be here any minute," Shinji advised.

"It doesn't matter; I won't survive either way." His eyes turned to Rei, "Rei, you have wondered why you were created, I shall tell you- for him." And he pointed at Shinji.

"What do mean for me?" the boy gasped.  Gendo actually smiled at him.

"When your mother passed away, there was no one left to look after you.  I was in no condition to take care of you, so I created someone who could watch after you.  Someone who could stand by you when you needed help or just listen to you when you had a problem."

"Commander, am I a clone of Shinji's mother?" Rei asked.  She had secretly wondered about this since the moment she drew her first breath.

"No, Ayanami, you are not.  I merely used my wife's cells as part of your genetic structure.  I wanted to create someone that Shinji would feel comfortable around, and who better than his mother."

Shinji and Rei looked at one another in shock.  They…they were supposed to be compliments of one another.  Rei was created just so Shinji would have someone to talk to and console him.

"Commander, why would SEELE want you dead?" Rei inquired.  Gendo was gagging by now, but he forced himself to stay conscious.

"I am the biggest hurdle that they had.  They wanted me out of the way so they could proceed with their plans."

"What do they want?" Shinji nearly demanded.

"To become the Ultimate Lifeform.  That is why they built the Evas in the first place- to understand what human beings could become if they were induced with knowledge of 'Adam'."

"Shinji, you must stop them.  If they succeed in creating such a lifeform, nothing will stop it; NERV, Tokyo-3, everyone will be destroyed."

"What should I do?  I can't defeat them on my own." For the first time in his life, Shinji saw Gendo look at him with affection in his eyes.

"My son…you have become the man that I wanted you to be; now, you must ask your mother for help.  She has been with you since you began to pilot Eva 01."

"Wait a minute!  You mean Eva 01 is…is…is…"

"Yes Shinji, it is your mother, Yui." Gendo coughed up his own blood, and he raised his hand.  Shinji took his offered hand and clutched it tightly.

"Father…please, don't leave me now."

"It's all right, my son, even though I will die, you will not be alone anymore.  Rei will be with you, and I'm sure that Asuka and Misato will stay by your side as well.  You aren't alone anymore so don't be afraid.  The only thing I ask is for your forgiveness, my boy- for being a pathetic excuse for a father."

"Of course, I do!" Shinji nearly cried.  Gendo smiled at his son.

"You have a good heart, Shinji, just like your mother.  Now please, finish the work that I started and free mankind from its own mistakes." Those were last words that Gendo Ikari uttered before his eyes closed for the last time.

"FATHER!" Shinji's cry could be heard in all of NERV.  His shoulders were shaking as tears fell from his eyes.  Rei put a comforting hand on his shoulder as she was meant to and let him let loose his emotions.

"Shinji!" a voice called from the doorway.  Misato ran into the room and skidded to stop when she saw the gruesome scene.

"Oh Shinji, I'm sorry." The young Ikari wiped the tears from his eyes and stood up.

"What is it, Misato?"

"We're under attack.  It looks exactly like an Eva.  It came right out of the depths of Terminal Dogma.  I've never seen anything like it.  Asuka is headed out now, but she can't handle it alone."

"Rei?" Shinji asked turning his head towards her.

"Let's go." Misato then noticed Shinji's left shoulder.

"Oh my gosh, your arm!"

"I'm fine, Misato.  Where's the Eva now?"

"It's about three levels below our control center.  If it hits that, we're all finished…" Shinji's eyes narrowed, and they filled with a determination that Misato had never seen before.

"This ends now!" He ran out the door, heading for the docks.

Author's Notes:  I apologize if my character traits or storyline are a little off.  I've only seen a few episodes of Evangelion so bare with me please.  I hope that you enjoyed this chapter cause next time, it's the final battle.