Chapter 3

A/N: I noticed that the last chapter was a bit sloppy, so I'll try to slow it down a little.

Also I forgot to say this last time; I don't own Neon Genesis Evangelion, but enjoy!

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Shinji sat in his bed, a cocktail of loathing and fear surging through his body. Shinji's father, Commander Ikari had just walked through the door. Immediately Shinji recalled the day his father abandoned him. Shinji was just a young boy, and Gendo had left him at the train station to be picked up by his relatives. That was the day according Shinji himself, when his life took a turn for the worse.

"Hello son." At first Shinji thought he was hearing things, so he blinked really hard to make sure his eyes weren't deceiving him. It really was his father, and his father had just addressed him as son!

Gendo walked over to the bedside then stopped and looked down with a sorrowful look on his face. He made Shinji jump with shock by suddenly speaking again, "I'm sorry son, this is my fault. I should have sent more test drones against the angel, to see what we were dealing with." Gendo paused, perhaps waiting for Shinji to reply. If Shinji had to save the life of Asuka, Rei, and Misato by uttering a single word at that moment, the three of them would be 6 feet under because Shinji was beyond speechless.

"Is this really my father?" Shinji asked himself, "He's being, kind."

And then his father did something Shinji thought he would never do, he affectionately patted his head, ruffled Shinji's hair in the process. "Its okay Shinji, you don't have to say anything, you should save your strength anyway. Just know this: I love you with all my heart, and if there was any other way to defeat the angels, I would scrap the Eva project in a flash. I told your mother before the accident that if anything happened to her, I would take care of you, and look how you ended up…" Gendo looked away and got up. "I'm glad you're okay, but I have to get going; I'm very busy you know. I just thought it would be nice to see you before I got tangled up at work." Gendo moved towards the door but before exiting turned his head and said, "And Shinji, despite what happened today, you did a good job." And with this Gendo left, having no clue how bewildered he left Shinji Ikari.

Shinji sat staring at the door looking what must of seemed like a cross between a barn owl, a deer in the headlights, and a wide mouthed tree frog all at the same time. Abruptly, Shinji noticed something that broke him out of his trance like state. He looked around and saw what he was looking for, the intercom. He pressed the button and a few seconds later the whiny voice of a nurse answered "Yes?"

Shinji, who was now beet red, replied, "I think I need a new set of sheets please."

20 minutes later the nurse who had come to Shinji's aid left the room clutching the soiled bed sheets muttering angrily something about not getting paid enough. Shinji had tried convincing the nurse he spilt a glass of water, but the lack of an empty cup and the smell emanating from the sheets was all the evidence required by the nurse to throw dirty looks at Shinji.

Now that the nurse was gone and he had a fresh set of sheets, Shinji could focus on the two troubling meetings he had. First Rei Ayanami; she had been waiting for him to wake up. This wasn't the first time she had done this. "She was with me when I woke up after my first sortie against the 5th angel." Shinji thought to himself. "But she didn't nearly strangle me in a hug when I came to; in fact she acted like she always did before. She didn't show any emotion and it barely seemed like she cared about my well being." But now she had, further than Shinji thought possible in the girl. If it had only been Rei, Shinji might have been able to ignore this personality shift; but then his father came into the picture. Shinji had no single memory of his dad showing any affection; hell, he had never called Shinji "son" before. Shinji couldn't understand how, after so many years of neglecting him, his father could act like "father of the year." Something was terribly wrong, and he was going to have to tell Misato about it.

A troubling thought came to mind when he thought about Misato. What if she was different too? If Rei and his father were different, what would stop Misato from being different? Before Shinji could dwell on this disturbing notion he was interrupted by a familiar voice; it was strong like he remembered but different too, soft.

"Shinji? Are you okay?" asked a voice full of worry. Shinji looked up to see the red haired girl he loved and feared at the same time standing in the doorway. Asuka looked almost afraid to come in. Shinji immediately noticed that Asuka too, was acting different, although he choose not to question her about it; there was a risk that she could return to normal and rip him a new one for being a nosy pervert.

"Asuka? Is something the matter?" Shinji asked, also nervously.

"Uh, no Shinji, nothings the matter" Asuka replied walking towards Shinji and pulling up a chair. They both sat in awkward silence, Shinji not knowing what to say. He wanted to ask her so many things, but was afraid because of the potential for a tongue lashing. So he chose to look down at his bed sheets and wait for Asuka to make the first move. He didn't have to wait too long, however."

"Baka!" Shinji actually gave a mental sigh of relief at her outburst. He looked up at Asuka, expecting to see the defiant look he was so used to, but instead was met with a look of nausea. The mental sigh that had been let out by Shinji did a 180 and crammed its way back into his head. So Asuka was acting differently too. "Just because you've always been the top Eva pilot, doesn't mean you have to be cocky when you fight the angels! Today I thought you were gone forever, I thought we would never speak again." The mental sigh back in Shinji's head was now tearing up what remained of his brain. Although he had thought, only moments ago, that anyone could be different, he wasn't prepared for this. Asuka never opened up to anyone, let alone him. She continued, "I know we don't get along because you don't like me, but know that I at least care about what happens to you." At this sentence, Asuka now looked extremely embarrassed. "Sorry Shinji, you must be tired, I'll leave you alone now."

"Wait!" was all Shinji could manage to say before Asuka had left. But she ignored him and now Shinji was alone and almost too overwhelmed to think straight. He adjusted his hospital bed so he could lie down and just sat there staring at the unfamiliar ceiling. Without thinking of anything Shinji almost drifted off to sleep…, but was interrupted by a loud scream

"Stay away from me; I didn't try to kill Shinji!" Shinji barely managed to register the blue flash that ran past his door as Rei, but guessed it was her by the battalion of orderlies and Section 2 agents that followed chase.

"That way, follow her!" was heard by Shinji as the pack made pursuit. "Great, another thing to worry about." Shinji sighed. But immediately the shouts of pursuit became shouts of panic. The mob that had been chasing Rei ran past the door again, but this time, all of them with a considerable look of fear on their faces. It looked like the group hit a choke point in the hallway because the last man in the group had stopped and started to yell "Hurry up she's…" but before he could finish a dart suddenly appeared on the man's back. The Section 2 agent managed to mumble "potato salad" before collapsing. A renewed roar of panic erupted from the group. A few seconds later Rei appeared in the doorway, holding what appeared to be an agents tranquilizer gun. She stopped at the doorway and put her foot on top of the fallen man, like a hunter posing with her kill.

Shinji managed to stutter, "R, Re, Rei, are yyyou alright?"

Rei responded as though she hadn't just knocked out a government agent, "Of course I am Shinji, but why is your voice getting deep?"

Shinji made a confused look on his face, his voice didn't sound any deeper. "What are you talking about, my voice…" but even as he was speaking, Rei's face gave a look of relaxation and she closed her eyes. She collapsed onto her stomach, revealing a dart protruding from her ass. Shinji painfully got out of the bed (he was still hurting from the days injuries) and limped over to Rei. He knelt down, but before he could do anything a disheveled Section 2 agent with a panicked look in his eyes came into the doorway. Before Shinji could say a word the agent fired the tranquilizer gun he was pointing at Shinji. Shinji looked down and saw a dart in his chest. He pulled out and before he slumped to the floor, he thought "This day keeps on going bad from worse… ughhh, potato salad."

A.N: That's chapter 3, in the next installment expect to find out more about the "Shinji version B" that the Shinji we know and love replaced. Also, I think that the whole "alternative universe" thing will be revealed to everyone (I'm not sure though).

Also if anyone cares, I mainly listened to the Eureka 7 OST while writing