Disclaimer: You already know.

AN: This one came out way longer than I intended. I kind of went into overdrive on this one.

AE.3

It has been a week since the girls' separation and so far, things were fine and back to normal. Asuka, her usual abrasive self and Rei, her abnormally calm self. Things were as they were before the incident, except that Shinji was more withdrawn than before. He missed Asuka's remarks totally and strangely became as quiet as Rei. Touji and Kensuke noticed this and tried to help him, but he gave no reply and often spent his time alone. Misato knew the problem, but hoped that time would eventually heal his wound, even one as large as this one.

However, time decided to take an unexpected leap...

Nerv HQ.

The three Children were preparing for their weekly synch test. Rei was already in her plug suit while Asuka just finished with hers. Shinji was the last to come out.

"Took you long enough. I don't have time to waste on you."

Shinji made no reply and Asuka stopped. As much as she didn't want to admit it, she was worried about Shinji. She knew it had something to do with whatever happened when they fused, but Asuka didn't remember. Glancing at Rei, she saw the First Child's gaze was also on Shinji. She's worried too...huh? Asuka blinked her eyes and looked at Rei again. Rei's face was neutral and placid, just like always. Yet Asuka could tell that she was worried. What the hell? Rei's eyes shifted toward her and she looked away.

She's worried about him. But how am I so certain of this? Rei had taken a glance at Asuka, who had turned away. But Rei knew she was staring at both Shinji and herself. What was strange was she knew that she was worried. It would have been the most logical choice that Asuka was worried, but Rei didn't have to choose. It was obvious. Mostly because Asuka's eyes reflected the same emotion. Emotion? A new emotion. Before either girl could contemplate further, all hell broke loose.

"Ahhhhhhhhhh!!!!!"

Shinji suddenly twisted around to see Rei hold her head, screaming. She began to tremble violently and crumble to the floor. Shinji instantly was with her.

"Rei, what wrong?"

She didn't answer as she continued to scream. Another scream suddenly echoed behind Shinji. Turning around, he saw that Asuka too was wrenching her head and screaming. Ritsuko heard the commotion and entered to find the two girls screaming on the ground. She checked Asuka and then Rei.

Shinji was beyond worried, "Doctor, what wrong with them?"

"I don't know." She turned and yelled at the others that had heard the screams, "Get them to the medical bay immediately!"

Medical Bay

Misato was called in and instantly rushed to the medical. There she found both Rei and Asuka in bed, with various instruments attached to them. Shinji was standing nearby, a great deal of worry clouded over his features.

"What happened to them?" she asked Ritsuko, who was comparing the data from the computer.

"I was afraid of this. It's a side effect of the fusion. They've existed as one for too long." She dropped the pad on the table, "It's gotten to the point where they can't survive without each other."

"Is there anything you can do?"

"The only way to stop this is the fuse them back. But it was an accident to begin with. I doubt that it'll work again."

"Can't we at least try?" Shinji asked.

Ritsuko looked at his worry filled face and softened, unnoticeably to the others, "Possibly. But it's uncertain."

Misato jumped in, "Better to risk it than to get two dead pilots."

Ritsuko shook her head, "One more thing. We still need Commander Ikari's permission."

"Permission granted."

Everyone blinked to see Commander Ikari standing behind them.

"Sir?"

"Do what you have to do, Doctor." His voice showed that it was final and he turned and left as swiftly as he came. Ritsuko was the first to shake out of her shock.

"Come on, let's hurry."

The two Children were loaded into the entry plugs of their respective Evas. Ritsuko, Misato and Shinji all watched from the control room as Ritsuko tried to repeat the same incident exactly.

"Synch ratios are unstable, but they show no signs of rising."

"Asuka, Rei. You have to listen. You have to synch thought. You did it before."

No response. Both girls were motionless.

"Life signs deteriorating."

"What was the last thing you remember before the last incident? Come on, hurry!"

"Nothing's happening. They're loosing brain functions. They're dying."

"Asuka! Rei!" Shinji yelled through the comm.

"Shin..."

"...ji."

Shinji blinked at the combined response and both pilots' eyes opened and fell upon him at the same time.

"Shin...ji...kun."

"Ba...ka..."

"Ratio rising rapidly. 150, no wait. 350%!"

Shocked, Ritsuko turned, "No, that way too fast."

The girls began to become transparent and they faded all together.

"Cut the power now!"

"I can't. The circuits have been locked out. Ratio at 399% 400%!"

The two Evas suddenly activated and broke free from their restraints. With loud roars, the Evas began to tear apart the hanger bay.

"Eject them now!"

Ritsuko glared at Misato, who had just given the order, "You can't..."

Misato ignored her, "Do it!"

The two berserker beasts were shot up though the hanger and onto the surface. This however did not stop their rampage as they began destroying the buildings around them.

"How do you propose to stop them now, Major?" Ritsuko didn't try to hide the distain.

Misato looked over at her briefly before turning to Shinji, who had been watching the events unfold, "Shinji. You have to go out there."

The boy's eyes widened, "What?"

"You have to go out there and stop them with 01."

Shinji took a small step back, "I can't fight them."

"I'm not asking you to fight them, Shinji. All we want you to do is cut their umbilical cords and hold them off. The reserve power will only last five minutes, so you have to distract them until then."

"Hold them off?"

Misato bent down and put her hands on his shoulders, "It'll be hard, but you can do it Shinji. I know it. They know it. She knows it."

Shinji stared silently at the monitor for a moment and then nodded, "Roger."

Moments later, 01 was launched up into the city. Already the two Evas had done a great share of damage and many of the buildings where toppled.

"Shinji, do you read?"

"Hai."

"You can use the progressive knife to cut the cords. Don't worry about movement. They've destroyed mostly the supply buildings. But you have to hurry before they get into any populated areas. Once you're done, you have to stall them, understood?"

"Hai."

"And Shinji. Be careful."

The progressive knife opened and 01 held it tight in its hand. The two Evas paid little attention to him and continued their rampage. Shinji looked around and found his first target. Moving swiftly, Shinji reached the first cord and brought the prog. knife down, cutting it.

"Shinji, look out!"

Apparently, the two Eva's noticed and now turned to attack. 02 charged first, at incredible speed. Shinji managed to dodge the strike, but it left him open to 00, who smashed a fist into his face. 01 reeled on the floor, dropping his knife and the two Evas charged again. Scrambling to its feet, 01 leaped out of the way of the two charging monsters and obtained the knife again. However, he underestimated the recovery speed of the Evas and 02 tackled him to the ground. Shinji tried to get it to rise, but the red machine was too powerful. Worse yet, 00 was approaching as well. Shinji then noticed that 02's cord was connected and nearby. Summoning the last of his strength, Shinji pushed 02 upward and cut down on the cord, slicing it. Shinji gave a short sigh of relief until he realized that the Evas were still functioning and they tackled him again.

"Ahhhhhhhhhh!!!!!!!!!"

"Shinji!"

Shinji continued to be hammered into the ground by the two Evas. Everyone watched in terror as 01 is being brutalized. Shinji is unable to fight back as the timer hit 1:30. Misato cringed. Too much time. And that only for the 00. He won't be able to hold out that long. 02 held down the battered Eva while 00 raises a fist and aims for 01's head. Shinji watched in horror as he sees the fist ready to finish him.

"Shinji...help...me."

That voice? Tsunami!

00's fist came down, but it was suddenly stopped short...by 01. The purple Eva had wretched its arm out from 02 and grabbed the fist. A low growl emitted out from machine-beast.

"I'm coming, Tsunami!"

"Shinji's synch ratio is rising. It's already at 300%"

The purple beast machine suddenly reared up and push both Evas down to the ground and held them in place.

"Shinji, wait!"

"It's going even faster. It's reaching the critical point. 400%"

Shinji's body began to become transparent and every feared that 01 would take him. But at the same time, a speck of light appeared where his chest was at.

"What... is that?"

The light grew brighter and brighter and soon the entire cockpit was filled with light.

"We've lost visual on Shinji"

"Look. The ratio is still rising. 650%"

"What? No, that's impossible!" Ritsuko exclaimed.

"750%! It's not stopping."

"1000%!"

"That...is...impossible. 1000%"

The entire Eva began to radiate as beams of light shot out. The section with the entry plug exploded with light and a figure arose. It was too bright to see at first, but as it rose higher, everyone gasped in shock.

"Shinji!"

Shinji floated out of his battered Eva glowing in pure light. A bright hexagon shimmered around him in pure energy and power. As he continued to rise, six wings, like that of an Eva, sprouted from his back. He hovered over to 02 and the entry plug automatically shot up and out. Raising his hand, Shinji ripped the plug open and moved closer. There, unconscious in the pod was the reformed Tsunami.

"Tsunami."

Shinji carefully picked her up and flew out again. He slowly lowered himself to the ground and when he touched it, knelt down.

"Tsunami. Please wake up."

The purple-haired girl remained motionless. Shinji began to shake her a bit.

"Tsunami, please."

Tsunami's eyes opened partly and she looked up at the angelic boy before her.

"Shinji..."

Shinji helped her up a little, "You came back."

"Of course. I promised you that I would."

A huge smile appeared over his face and Shinji's eyes began to fill with tears, "I..."

Tsunami however touched his lips with her finger, stopping him.

"I know." she smiled.

Shinji smiled even more and the AT field as well as the glowing wings vanished. Shinji's eyes began to droop and they closed altogether and he fell unconscious. Tsunami merely cradled his head against her breast and softly cradled it.

"Rest, Shinji. I'll be here."

The command crew was completely silent as they watched all of the events unfold before them. Some had smiles on their face, (Misato-major smile) while the others were merely dumbfounded. Only Commander Ikari seemed the same. However, beneath the folded hands (and unseen to all eyes), a large grin was on his face.

________

Gendo's Office.

The Commander and Sub-Commander were playing a game of chess.

"Well?"

"The Third Child is recovering, along with Tsunami."

"The awakening was earlier than expected, but so much the better."

This obviously caught the sub-commander off-guard, "What?"

"Now that he has awakened, my role in this is now over."

"What do you mean 'your role'?"

Gendo moved a piece, "Actually, it's Nerv's role. What its true purpose was. The point in which the Messiah will come. 'And they will prepare the way of their savior.' 'From the belly of the beast, the Messiah will arise; the second Adam to save humanity.'"

"The Dead Sea Scrolls."

"Project Eva was just a way to battle the angels until his awakening. To that end, I have done everything according to that."

It was Fusuyugi's turn to move, "Explain"

Gendo analyzed the move, "Love is a very powerful emotion, one that I used accordingly. The Third Child had to bond with someone; had to love someone in order to awaken. The Major was enough to have as a parent and his friends would help, but he needed more. He needed to love someone so much that he wouldn't think twice about saving them. That was why I created Rei."

"Rei...was a part of this?"

"I used what I could to create Rei. Her image, I altered in order to look similar to Yui, hoping that he would bond with her on sight and develop a relationship. However, I made a crucial error in training and I failed to take in the psychological factor so I tried another source." He made another move on the board.

"Asuka."

"You don't think it was a coincidence that she was the Second. They say opposites attract. Unfortunately, she was too harsh for him. However, in his seeming vulnerability, his true power came to light. Each time he pilots, he grows stronger simply by his desire to save his loved ones."

"You knew this would happen to him the entire time. You mean the scenario you shared with me was false?" His move.

"No. More like Plan B. However, the girls' fusion made it all possible. She succeeded in awakening him."

"If these things were true, then why not care for him yourself? He is your son."

"He is also a painful reminder of what I lost. I couldn't face that. So instead, I became his enemy."

"And in doing so, made him more likely to turn to someone else."

"He needed to be stronger. I did what I could. And the results were just as I predicted."

"What about the Angels? And SEELE."

"The Angels will not be able to stop him. His powers will be more than enough to defeat all the remaining angels. He is the true weapon to stop them. As for those old men, I have already taken the appropriate steps."

"And then?"

"Then I'll trust Shinji to complete the work he has in store for him."

"Curious. These are not the words, nor the plans of a scientist. And you called him by his name now."

"Correct on all accounts." Gendo finally made his move, which turned out to be the last in the game.

"Checkmate."