Disclaimer: Same as before.

Chap. 3

Shinji was surprised and the older Ikari smiled a bit. A weakness.

"What does mother have to do with this?"

"It has everything to do with this. The angels, Nerv, Eva. Even Third Impact. All of it is based for her. You now have you answer."

"I don't understand."

"And you never will."

Shinji gave a resigned look. Mother. I don't get it. What does she have to do with...Third Impact?

"Tell me about Third Impact."

________

Outside his office…

Misato had just arrived at the HQ.

"What's going on?"

Fuyutuki walked to her, "We believe Shinji has locked himself in with the Commander."

"What? Why?"

One of the guards by the door answered her, "We don't know. But it won't matter. We should be able to get in a couple of minutes. Then we'll let the Commander decide." The guard looked back at her, "But you can bet that he won't tolerate insubordination."

Misato thought to herself. What was he thinking? He has no idea how much trouble he's in.

_______

"Do you really want to know? I warn you. Few have lived knowing the full truth. And to be honest, you don't deserve to know."

Another shot rang, getting very close to Gendo's other side.

"I will decide that."

Gendo twitched. The more they were like this, the more Shinji began to remind him of himself. To an extent...

"SEELE is the organization behind Nerv. They exist in the shadows of the UN. They are also behind the Human Instrumentality Project."

"Instrumentality Project?"

"When man transcends to a higher plane of consciousness and ceases being man. In a sense, man becomes the final angel. Third Impact."

Man....the final angel?

Gendo stared, Good, his defenses are breaking down. "Angels seek to unite with Adam, the first angel. Once that happens, Third Impact will commence. SEELE will attempt to use Third Impact in order to control the world."

Shinji began to stumble back. At that moment, Gendo managed to pull a second gun out and point it at Shinji. However, Shinji didn't seem to notice...or care. Both Ikari's simply held a gun on each other.

"So that's it? All the fighting...all the pain and suffering, just so that you and a couple of guys could control the world?"

"I knew you wouldn't understand. It's beyond your comprehension."

It doesn't make sense. Surely there had to be another reason. Then it hit him. It was so clear now. His battles in the Eva, the way it acted, even the disturbing comfort he felt from piloting it.

"You didn't explain what it had to do with mother."

Gondo blinked, So he caught on. "No, I didn't."

"This has something to do with that day, doesn't it? When she...left…" Shinji straightened up, "Why do you want Third Impact?"

Gendo's eyes widened. Another unexpected. He didn't think Shinji would be able to deduce his motive from that kind of info. He only told him about Third Impact and SEELE simply to weaken him. But now he's coming close to learning the truth. Too close.

"I believe that's enough. You've served your usefulness."

Shinji lowered the gun, "If you wanted to shoot me, you would have done it already. But you need me. And the only reason for that is that I would be needed to pilot the Eva again. Asuka is comatose and Rei can't synch well with either units, so you need me." He looked up, "Or rather, you have a use for me."

The door behind them began to lurch slightly. Gendo looked at his son, no, his subordinate. He never knew his son.

"That is correct."

The door behind began to lurch a bit more and fell down altogether. As the guards stormed into the room, Gendo and Shinji faced each other. Shinji looked at his father, no the commander. He ceased to be his father a long time ago.

"She would never have wanted you to do this. You're making a mistake."

"Take him away."

Misato came in as well, "Commander, no!"

"Major Katsuragi, Pilot Ikari has committed a grave offense and must be punished as so. You know that full well."

Misato cringed, but she held fast, "But, he's your son. Surely, you can't..."

"Major. Do not question my authority."

Shinji turned to her, "Misato, its fine. I knew what I was getting into when I did this. Don't worry about it."  He looked at the Commander and for the first time, with eyes of pity, "I found what I was looking for. I...understand."

With that, the Section 2 guards took him away, leaving Gendo to himself once again, aside from his second, Fuyutuki.

"Ikari."

"Don't. I've been tested enough as it is."

___________

Meanwhile, the guards and Misato were taking Shinji to his cell. They had to pass the Eva cages to get to the elevator. As they did, Shinji looked up at 01. So this is it. The end. Mr. Kaji was right. It doesn't matter if I die, so long as I know the truth. He looked over to Misato who was looking back at him it a sad face. Sorry, Misato. I won't cause you any more pain.

Awaken.

Shinji suddenly flashed and his body glowed in a strange light. The light shone and the guards were pushed away by some kind of incredible force. Misato managed to back away as Shinji continued to glow in an aura light that began to solidify in a hexagonal shape, one that was familiar to the major.

No way. That's… that's…Shinji is producing… an AT field?

Shinji too was in shock, not knowing what was happening to him. But somehow, he knew it would. It was as though something inside him had awakened. Then he remembered what Karowu once said...

What you call AT field is merely a person's soul. The place around a person that can't be penetrated by anybody.

"Shinji?"

Shinji looked at Misato who was staring at him in shock. He wanted to say something, but a sudden rumbling caught his attention...

Control room...

"Emergency. We have an emergency."

"What is it?"

"Eva 01 is activating on its own."

"What?"

Eva 01 began to struggle against the restraints and eventually tore them off. The purple machine/ creature then turned around to Shinji and held out an open hand. Shinji began to move toward it.

"Shinji, what are you doing?"

Shinji looked back at her, "I have to go now, Misato."

"What? Where? Why? Don't run away."

"I'm not running, but it is too dangerous for either me or 01 to be here."

She was baffled, "What do you mean?"

"I can't tell you. Honestly, I'm not even sure. Not yet. You have to trust me."

In the command center, Commander Ikari watched the scene with 01 and his son. 01 began moving again with Shinji held in its right hand.

"Cut all elevators."

"Yes, sir."

01 continued to move around, although it had nowhere to go now.

"Prepare to retrieve unit 01 and to apprehend the pilot."

"Sir, something's wrong. The synch ratio is rising!"

"What?"

Looking back at the screen, they saw the aura around Shinji beginning to glow brighter.

"75%, 85%, 100%, 125%. It's rising at an incredible rate."

"That's impossible! He's not even in the entry pod!"

"200% 250%, 310%. He's reaching critical!"

The back of Eva 01 opened and golden wings sprouted out

"Huh? He stopped at 399%"

Everyone breathed a sigh of relief, but that was before unit 01 roared and jumped into the air. Gendo saw its direction and knew where it was heading.

The Terminal Dogma…

Gendo turned around and headed slowly out. He still had one more move.

Unit 01 flew downward into the sea of LCL. Standing before him was Lilith, the second Angel. 01 seemed to regard it for a moment, just standing there. A shimmer of energy began to form around 01, an AT field.

"Shinji."

01 turned around to see Commander Ikari standing on the deck below with a gun in his hand. And standing in front of him was Ayanami Rei.

"Ikari, I give you this final choice. You are to stand down and surrender."

He didn't have to finish. Shinji knew what he going to if he defied him. Shinji was distraught. He didn't plan on this happening. His father was now in control again. No, not Rei. Shinji thought of attacking, but there was no way he could stop him without hurting Rei.

"Stand down now!"

Shinji looked at his father, and then at Rei. It was then that he caught Rei gaze. She seemed to look blankly at him, but her hand moved to the necklace he gave her.

Thank you for always being you, Rei-chan.

01 suddenly moved toward them. Gendo expected that he would try and rescue her. Still predictable. The gun hand twitched slightly, just enough for him to see it as 01 continued to come at him. But suddenly, 01 flew straight up into the Geodome and shot out through the surface.

Control Room…

"Shut it down immediately!"

"We can't. All controls to 01 have been cut off."

"Track it."

"I can't. It is somehow disrupting our tracking devices. It's gone, sir."

Fuyutuki hands tightened, Gendo isn't going to like this.