"Shinji-kun!"

Misato watched the monitors, displaying Shinji inside his plug. Bubbles rapidly fizzed upwards, the LCL becoming superheated.

"Get him back inside! Now!" Misato yelled.

The floor beneath Unit-01 collapsed, sending the Eva down with it. The Angel's beam quickly stopped.

"The target has become inactive," Aoba said.

"How is Shinji?" Misato asked.

"EEG abnormal! Pulse faint!" Maya said.

"Unit-01 headed to cage #7," Aoba said.

"I'm going to the cage! Ritsuko, send the medic team ASAP!" Misato yelled, rushing out of the command center. Rei silently watched the scene unfold before her.

"Pulse has stopped!" Makoto yelled.

"Life support to maximum! Begin heart massage!" Ritsuko ordered.

Shinji's breastplate sent multiple powerful waves directly to his chest.

"Pulse confirmed!" Makoto said.

"Emergency eject plug, drain all LCL!" Ritsuko commanded.

Shinji's plug spun out of the Eva's neck, jets of LCL pouring out the side as medic crews hurried to extract him. The hatch opened, and more liquid flooded out of the plug.

High above Central Dogma, the Angel began to extend a pink drill towards the ground. It punctured the pavement, and slowly dug down into the earth.

"What is the target doing?" Ritsuko asked.

"It's beginning to drill down into HQ!" Aoba said.

"It's trying a direct attack against us?" Ritsuko replied.

'Where am I?' Shinji wondered. He floated inside a white void, blank and featureless.

'I don't think I'm dead,' he thought. 'Every time I get in this thing, I get hurt. It's not fair. Why am I doing this?' he again asked himself. 'For who?

Shinji saw a shape approach him, undefined and vague. It had the form of a human but was shifting and morphing as if made of putty.

The shape took the form of his father. Shinji wanted to laugh, but he took in the expression on his face. He was smiling. Smiling for him, because he was proud. It was a sight completely alien to Shinji, and one he had wanted to see desperately for over ten years. It vanished as soon as it took shape, returning to an undefinable mass.

The shape then took the form of Misato, happily holding Pen-Pen as she smiled at Shinji. Even in just a few short weeks, he had come to care for his surrogate family. He couldn't leave them to die, Shinji knew that. As difficult as piloting the Eva was, it wasn't as bad as being abandoned again. She too vanished quickly.

The shape took another form, one Shinji did not recognize. She had short brown hair, like him, and green eyes. She was wearing a lab coat. She smiled at Shinji warmly. He didn't quite understand who she was, but he felt a familiarity with her.

"...Mom?" Shinji mumbled, waking up in a hospital bed.

Shinji looked to the side and saw Ayanami. She was looking at him, clearly having heard what he said.

"A-Ayanami?" he asked, wondering what she was doing here.

She pushed the tray by his bedside towards him. "Here's some food. They said for you to eat something once you woke up," she said.

"...I don't feel like eating anything," Shinji said, sitting up.

"I think you should eat something before you go," she said. "We leave in 60 minutes."

"Huh?" Shinji asked.

Rei held up a small notebook. "This is the schedule for the operation that begins at zero hours tomorrow," she said. "Shall I read it?"

She didn't wait for him to respond.

"Pilots Ikari and Ayanami will assemble at the cage at 1730 hours. At 1800 hours, Eva Units 00 and 01 will be activated. At 1805 hours, launch. At 1830 hours, arrive at the temporary base at Mt. Futago. Await further orders."

She put down the notebook, looking at him from across the tray of food.

"I have to get back in that thing, don't I?" Shinji asked, knowing the answer.

"If you don't want to, why not just run away again? I can pilot Unit-01, it won't take long to rewrite the personal data."

Shinji stared at her, a little annoyed. 'She can act so condescending sometimes,' he thought.

"Well then," she turned to leave, "I'll see you in 60 minutes."

She left the room.

"Make sure you eat something."

The door slid shut.

Operation Yashima was well underway, and Misato was making the final preparations before go time. She had politely requested the JSSDF relinquish their experimental positron rifle and shield, deeming them both more valuable in NERV's hands. Tokyo-3 had long been evacuated, and emergency broadcasts were flashing across the whole country notifying the public of an induced blackout beginning at midnight.

The bridge crew had relocated to a van outside of the city, their temporary base far less glamorous than Headquarters. Maya did not seem to mind Ritsuko being pressed against her. Positioned on a hillside road, a line of dozens of cars and cables wound back and forth up the switchbacks, culminating in a massive power relay at the summit. This is where they would make their stand.

"Target has breached armor plate #17," Aoba announced.

"Three hours fifty-five minutes until the final plate has been breached," Makoto said.

"Transmission link from Shikoku and Kyushu complete," Maya added.

"Begin test run on all cooling systems," Misato ordered.

"All right, listen up," Misato said to Rei and Shinji.

"This is a positron rifle," she said, pointing to the building-sized gun at the end of the lot they were in. "It's an experimental weapon, but according to our calculations, it can punch through the Angel's A.T. Field, even at this range. However, it's a precision weapon, and we've thrown it together on short notice."

"Now," she said, pointing to the equally massive shield nearby the rifle, "We jury-rigged that from the bottom of a space shuttle. It should be able to withstand the enemy's beam for 17 seconds."

"Shinji will be the gunner in Unit-01," Misato said.

"Yes, ma'am" he replied.

"Rei, you will be defense, in Unit-00."

"Yes, ma'am," she said quietly.

"This is because Shinji and Unit-01 have the higher synchronization rate. This operation requires a high degree of precision." Ritsuko explained. "Shinji, positrons are effected by earth's gravity, rotation, and magnetic field, they won't travel in a straight line."

"But I haven't trained for any of that," Shinji said.

"Don't worry, just do it by the book. When the indicators line up, pull the trigger. The MAGI will do the rest," Ritsuko reassured.

"What happens if my first shot misses?" Shinji asked.

"Just focus on taking out the enemy with the first shot," Ritsuko said.

'In other words, we'll be screwed,' Shinji mused.

"It's time, you two. Go get changed," Misato ordered.

"Yes, ma'am," they both said in unison.

Rei and Shinji waited by their Evas, a large chasm separating the two platforms they sat on. The moon shone brightly now that the light from the city no longer drowned it out. Every star in the sky was visible.

"I guess we might be dead soon," Shinji said.

"Why?" Ayanami asked.

"How can you be so calm?" Shinji responded. "You've been put through so much already," he said.

Ayanami didn't respond, she was staring at the moon.

"Why do you pilot the Eva?" Shinji asked.

Ayanami took a moment to reply.

"It's my link," she said.

"To my father?"

"To everyone."

"You're very brave, Ayanami," Shinji said.

"I have nothing else," she replied. "It's like I was born to pilot Eva. If I didn't have it, I would have nothing. That's the same as being dead."

Shinji thought about that.

"I guess I was like that before I came here," he said. "I didn't care about anything. But I didn't think about it. It was just easier to go through the motions of living."

'Why am I telling Ayanami this?' he thought. 'Is it because we're in the same situation? No. Maybe it's because it feels like she has even less than I do.'

Ayanami stood up.

"It's time," she said. "Let's go."

Shinji stood up, looking at the moon above them.

"You won't die," she said. Shinji looked over at her.

"I'll protect you. Farewell."

"Commence Operation Yashima!" Misato ordered.

Shinji was in position, the positron rifle in his hands. Rei stood in front of him, shield at the ready.

"Shinji," Misato said. "We're entrusting all of Japan's power to you."

"Yes, ma'am" he replied.

"Commencing primary connection. Begin transmission of power from blocks 1 through 803."

The power relays buzzed to life, lighting the sky around them blue.

"Voltage rising, increasing pressure!" Maya said.

"Cooling systems at max output. Positron influx nominal," Aoba added.

"Secondary connections complete! Accelerators are engaging! Activate convergence unit!" Maya yelled.

"Release final safety systems!" Misato ordered.

"Tertiary connections nominal. Cock the hammer!" Makoto told Shinji.

Shinji pulled the hammer on the rifle, inserting a charge into the barrel. The targeting reticle descended over his eyes, magnifying onto the Angel from across the lake.

"Seventh and final connections established. Error corrections for the earth's rotation is +0.0009"

"Ten seconds to discharge. Ten, nine, eight, seven, six…"

"High energy readings from the target!" Makoto yelled.

'Dammit. If we can get a shot off first, we still may have a chance,' Misato thought.

"Two, one…"

"Fire!"
Misato yelled.

Shinji pulled the trigger, and the positron rifle fired, erupting in a brilliant beam of green light. At the same time, the Angel fired, sending its own beam out as well. The two positrons met, and tangled above the lake, sending waves flying. They both continued and missed their targets.

Shinji tried to shield himself from the blast, and the bridge crew lost their footing as the van was topped over.

'Shit,' Shinji thought. 'I missed!'

The Angel's drill breached the Geo-front, sending buildings falling to the ground below it.

"Shinji! The second shot! Hurry!" Misato yelled.

Shinji cocked the hammer once more, exchanging the fuse.

"Another energy reading from the target!" Aoba yelled.

The Angel fired, and this time it didn't miss. The beam headed straight towards Unit-01. Shinji braced for impact.

"..."

He opened his eyes.

"Ayanami?" He said, seeing Unit-00 shielding him from the blast. Plasma was being ejected from in front of the shield, making the water in the air around them turn to steam. The shield was melting, and so was Unit-00.

"Ayanami!" Shinji yelled, moving the rifle back into position and waiting to fire.

"Hurry," he said, "please!"

He was being blinded by the light from the beam, but his aiming reticle slowly zeroed in on the Angel.

"C'mon, c'mon!" he yelled.

The shield broke, and Unit-00 began to take the full brunt of the beam.

"Ayanami!" Shinji screamed. The indicators finally aligned, and Shinji pulled the trigger.

His aim was true, and the positron beam penetrated all the way through the target, sending a jet of flames out the other end. Its own beam was stopped, saving Ayanami from further harm.

Shinji ripped of his targeting reticle and threw the rifle away, running towards Unit-00. He lifted it up, and cut open the entry plug hatch, seeing it emerge from the molten armor of Unit-00. He pulled it out and set it on the ground.

Shinji ran up to the plug and began to pull it open, his hands burning against the white-hot metal of the plug. He grunted as the lever gave way, ejecting a jet of steam around the hatch edge. He scrambled inside.

"Ayanami? Are you okay? Ayanami!"

Rei opened her eyes, Gendo's glasses falling from her hand. She saw a shape above her and got a powerful sense of deja-vu.

'Commander Ikari?' she thought.

When her vision cleared and she was presented with his son, she was surprised.

"...Ikari?" she said.

"Ayanami..." Shinji said, and his eyes began to well up with tears.

"You're crying again," she said.

Shinji looked at her.

"You were crying in your sleep in the hospital. Why are you so sad?" she asked.

"Dummy," Shinji replied. "I'm crying because I'm happy you're alive."

"Because you're happy?" she said, mostly to herself. "So you cry when you're happy, too."

Shinji looked hurt at that.

"I'm sorry," she said. "I do not know what to do at a time like this… even though I am also happy."

"Well, if you're happy," Shinji stated a small smile on his face, "then you should smile."

He reached out his hand to her. "Can you stand?" he asked.

Rei slowly sat up, and gingerly took his hand, feeling how warm it felt. She got up and smiled warmly.

"..."

He was staring at her.

"What's the matter?" she asked, snapping him out of it.

"Um, nothing!" he said quickly and helped her get up by putting her arm over his shoulder. The two of them walked out of the plug, waiting for Misato to arrive.

"Ayanami," Shinji said, as the two of them sat in a small clearing near the lake. The moon reflected in the water, lighting up both their faces.

"You should stop saying sad things like 'farewell' every time we go on a mission… it's too sad. We might not have anything but the Eva's right now, but… as long as we stay alive, one day we'll be glad we did."

He looked at her, smiling, and trying to remember the rest of the short speech he had planned if they survived.

"It might be far in the future, but until then, let's live on. Even on a black and empty street, if we go together, we might find something one day… like the moon that floats in the darkness."

Authors Note:

This is the end of the first chunk of this story. I'm gonna try to use more of my ideas from this point on, this is also where more of the relationships are gonna be developed. But the first arc of this story is so good already that I wanted to leave it relatively untouched, other than merging the show and manga into something I think is better as a whole.

Anyway, PREVIEW:

Mari and Asuka arrive in Japan, turning Shinji's newfound sense of normalcy upside down. Israfel can split in four, and all of our pilots must synchronize together to beat it. Kaji's advances towards Misato are halted (for now.) Shinji and Rei grow closer, only partially due to Misato's meddling. The Ingenuity of God falls from the heavens, and Shinji may have said a little too much while he thought they were all about to die. Tune in next time!