DISCLAIMER: I still don't own Evangelion or any of the characters, they're still property of…well, whoever owns them these days. This fic's got nothing to do with Rebuild, just the original series/movies. Timeline places this sometime after the 16th Angel, but before episode 24. It also borrows a fair amount of ideas/scenarios from the Bourne franchise, just so you know. And lastly, 'this' is thoughts and "this" is speech.


Chapter 1: Blues from a Gun

'Another damned rainy night,' the old captain thought grimly. The rain had been hard for several nights now with no sign of letting up soon. Sighing, the man took out a cigarette from a pack. He was about to light it when a strange sight in the water stopped him. 'What the hell…' he thought, reaching for the binoculars around his neck. A look through them confirmed what he thought: a body was floating about in this miserable weather. "Hey!" the captain shouted to the crew. "Get your asses out here! We've got a floater!"

After steering the boat around to the body, a couple of the fishermen threw a net overboard and picked it up onto the deck. The captain looked over it, a boy not older than fourteen or fifteen. He was dressed in a form-fitting full-body black suit that covered up to his neck. Then he noticed the slow rise and fall of the young man's chest. "Holy…" he said with a start, "he ain't dead yet." He then motioned for the two men who'd pulled the boy from the water to get him below deck and into the makeshift infirmary onboard.

Upon getting him down there, the ship's doctor examined the boy. On his back were two small wounds, apparently gunshots. Cutting away the plastic-like fabric of the suit, he proceeded to administer anesthesia to the young man and remove the bullets. One had struck him in the lower part of the left shoulder, nothing more than a flesh wound with a round inside. 'Easy enough to pry out,' he thought as he used a pair of pliers to do the job. The other, however, struck him in the shoulder blade, a few inches from the spine. Pulling out the round, the doctor discovered that the second round had struck something within the boy's skin. Cutting a little deeper, he found a strange microchip attached to the muscle near the backbone. The round had nearly missed it, only barely catching the edge. Cutting away the small wires attaching it to the muscle, he looked at the device carefully, not having a clue what he was seeing. His gaze lowered down to the boy, he mused, "Now what the hell do you make of that?"

Shinji Ikari's eyes snapped open, his body sitting bolt upright. Immediately, he regretted this action as a wave of pain coming from his back made him fall right back onto the small bed he occupied. Gritting his teeth to block some of the pain, he looked about the room. 'Where…where am I?' he thought. It certainly wasn't his room or the NERV infirmary, that much was certain.

"Ah, glad to see you've come to," an unfamiliar voice came from across the room. At the sound, Shinji nearly jumped out of bed, the motion sending another ache through his person. "Sorry 'bout that, didn't mean to scare you half-to-death," the voice continued. Casting his gaze towards the sound, the boy was met with the sight of a middle-aged man dressed for cold weather.

"W…who are you? Where am I?" Shinji asked, eyes wide.

The captain sat down in a wooden chair close to the door and sized up the young man his crew had pulled out of the sea. "Name's Mathieu," the man started. "and you're on my ship. Damned lucky we saw you, y'know?" As Shinji tried to sit up again, the captain noticed the pain in his expression. "Hey…take it easy for a bit," he started, lighting a cigarette. "Not everyone lives from gunshot wounds, y'know?"

Shinji's expression dropped further, his eyes remaining wide. "G-gunshot?" he asked.

"Yep," Mathieu answered. "Two of 'em, probably a .22 by the size." The quiet in the room lasted for a minute before the man decided he needed at least a few answers from his guest. "So…what's your name?"

Shinji winced again as he sat up and thought over his answer. "S…Shinji, sir," he said.

"Shinji, eh?" Mathieu asked, getting up from the chair and walking over to a cabinet on the other side of the room. "Well, I'll say this," he said, pulling out a bag and placing it in front of the boy. "There's some strange things you came onboard with…"

Looking into the bag, Shinji saw a couple of items that puzzled him. One looked to be a plug suit, black-colored and cut into two. The other was a dented and fried computer chip with some blood on it.

"Not even sure where to begin with either one, to be honest," Mathieu said. "How 'bout you?"

Shinji shook his head. The plug suit looked to be the same as the one he wore for tests and battle…but it was missing the neural connectors and the life-support device on the arm. The top half showed two small holes near the left shoulder on the back, the same place as the pain he was feeling. The chip, on the other hand, he had absolutely no idea about. "Never seen either before," he said. "This…came out of me?" he asked, holding the chip.

"Yeah," Mathieu said. "If I had to hazard a guess, I'd say it was a GPS tag."

'Something NERV probably did,' Shinji thought with a sigh, shaking his head. "Where'd you say you pulled me from?" he asked.

"A couple-dozen miles from the Tokyo-2 shoreline," Mathieu answered. "Dunno how long you were adrift, though."

Laying back down, Shinji felt at a loss for what he'd been told. 'Shot and adrift at sea…' he thought. 'What the hell was I doing out there?'

"Me and the guys are glad you came around," Mathieu said after a long silence. "Been worrying you wouldn't pull through…"

Shinji's gaze fixed back on the older man. "Wha-" he started, "how long have I been here?"

Mathieu tried as best as he could to hide his expression from the boy. "Almost five weeks…"

Shinji's eyes widened as much as they could. 'Five weeks…' he thought. 'Misato must think I'm dead or something,' he mused, feeling sorry for what he'd probably put her through.

"So where're you from?" Mathieu asked. "I can already tell you're from this country, at least…"

Shinji closed his eyes and sighed. "Tokyo-3," he said after a moment.

Standing up, Mathieu walked over to the boy and put a hand on his unhurt shoulder. "Ah, that's good then," he said, "we'll be pulling into Tokyo-2 in a week or so. Not too long a walk to home from there, huh?"

Shinji shook his head. "No sir…" he said quietly as the captain headed for the door.

Just before he exited, Mathieu turned back to the young man. "I get the feelin' you're not tellin' me everything. But I understand, man's gotta have some secrets, right?"

With the captain having left the room, Shinji stared at the ceiling for quite some time in silence. His life had been turned in some rather dark directions lately…but whatever had happened to him he couldn't even fathom. 'Everything's just as skewed as after the last few Angels,' he thought bitterly. 'But what in the world was I doing out there?' Sighing heavily, he pulled the sheet on the bed up and tried to shut out the pain in his back. 'At least it's a pain I'm used to…'

Eight days later, the ship pulled into the harbor at Tokyo-2. Waking up that morning, Shinji put on a t-shirt and pants one of the shorter crew members had donated to him along with a pair of shoes. 'A little big, but they'll do,' he thought. The pain that had been with him since he awoke on the boat had subsided a bit, making him able to get around with no problem. Leaving the makeshift infirmary and getting out onto the deck, the boy was met by the captain.

"Well lad," Mathieu said, holding a hand outstretched. "I suppose this is where we part company, eh?"

Smiling as best as he could at the man, Shinji accepted the handshake. "Uh…sure. Thanks for everything, sir," he said. "I only hope I wasn't a burden…"

"Nonsense!" Mathieu insisted, shaking his head. "Always feels good to help someone in need," he finished, handing the boy a raincoat. "Consider it a final parting gift. Rain'll be coming back soon."

Nodding to the older man, Shinji accepted the garment and put it on. "Hope to see you again one day," he said, walking towards the landing plank.

"Of course," the captain agreed. "It's a wide world out there, and you just never know…"

With a final wave, Shinji stepped out onto the docks of Tokyo-2. The smell of salt was strong in the air, the city certainly seeming more alive than Tokyo-3 'Not really a surprise considering…' he mused, walking out into the city. 'Most of the city's population had come here after what happened to Unit-00 because of that last Angel,' his thoughts continued, feeling the sadness come up again.

Several hard rain drops shook the thoughts from his mind momentarily. Pulling the hood over his head and resuming his walk, Shinji soon came upon a bank of payphones. 'Might as well try,' he thought, pulling a few coins out of his pocket and putting them in one of the machines. As the rain started to pick up, he dialed the number for Misato's apartment. Several rings later, the familiar answering machine picked up. Sighing, he hung the phone up and leaned against a wall nearby. 'Great…looks like I'm walking,' he thought with a hint of sarcasm.

After a few hours worth of walking, Shinji had begun to notice things he hadn't before. For one, he was avoiding people more than he usually did. 'Not that that's a whole lot,' he had thought once or twice. But it seemed like more like instinct to him now, not the deliberate avoidance he'd done so often. The further he got into town, the more he was heading off the beaten path and into the side streets and alleys. And for the life of him, he couldn't understand it.

Another had been the way he was sizing up people who had been curious. 'Dunno what the hell that was all about,' Shinji mused. The funny thing was, he felt confident none of them could take him in a fight. And that thought had felt like a gut-punch. He'd been in very few real fights in his life, Angels battles notwithstanding, and none of those he'd won…so he had no clue where these odd trains-of-thought were coming from.

"What's going on with my mind?" Shinji asked quietly, standing in a dark alley with the rain pouring down on him. Looking around, he saw a newspaper machine. Curious to know exactly how long he'd been 'lost', he walked over to the machine and saw the date. 'It's like he said, just over six weeks…' he thought, eyes wide and not having the slightest idea what had transpired. 'Maybe a battle went badly?' me thought, resuming his walk out of the city limits. 'No, Angels wouldn't use human weapons.'

And that was a main thought that'd been with Shinji since he awoke over a week ago: who in the world would've tried to kill him? NERV wasn't really under fire from anyone, as best as he could tell. Hell, they were saving mankind from the Angels. "So…why me?" he thought aloud. He'd also wondered about Asuka and Rei, if any attempt had been made on their lives. 'God, I hope not,' he thought. Although recent events had (for lack of a better word) soured things between everyone, he still didn't want to imagine his friends hurt or worse. 'Not that things could get a whole lot worse,' he thought with a heavy heart.

After leaving the city limits of Tokyo-2, Shinji spent the next day-and-a-half in the forests between there and Tokyo-3. Partially for natural cover, partially to avoid anybody else. "Guess that time camping with Kensuke taught me something," he said while seated at the foot of a large tree. "Should really thank him for that one of these days…"

Night had fallen, and Shinji had built a fire nearby the tree's base with whatever dry wood he had found. It provided some heat, but he was still quite cold. 'Feels like summer every day,' he thought, 'but nights can get pretty chilly. At least it stopped raining.' And while that was some solace, the moisture and chill in the air had done their best to keep the heat out of the boy.

Facing the fire and pulling the raincoat around him, Shinji prepared himself for what was sure to be another fitful night's sleep. "Haven't been sleeping well since I came to, actually," he mused aloud. That much was certainly true, the nights since then had been restless for him. The dreams were fractured, not really making much of any sense, and they'd be gone not long after waking. But deep down, he knew they were about whatever had happened to him…

Several miles from Shinji's nightly stop, a phone rang in a large office.

"Yes?" a man's voice answered.

The voice on the other end talked for a half-minute before falling silent.

"I see…continue keeping watch," the voice spoke again. Returning the phone to its cradle, it spoke up again to another in the room. "The Third Child was spotted in Tokyo-2 two days ago."

"Is that where I should go?" a soft feminine voice asked.

"No," the man's voice answered. "We know where he'll be going. Head there and give him his…homecoming."

"Understood," the female voice said. Several seconds of footsteps echoed through the large office before the sound of a door opening and closing is heard.

"Is it wise to send only her?" another voice asked.

"Have faith," the man's voice replied, the smirk nearly audible. "She'll take care of it."

The following evening, Shinji made it back to the outskirts of Tokyo-3. Looking out over the lake created by Unit-00's destruction, he felt the same heavy sadness come over him. Shaking his head of the thoughts, he mused, 'No time for that right now. I need to get back to Misato's.'

As he had done in Tokyo-2, Shinji took the most out-of-the-way path back there. 'Like my mind's telling me to avoid being seen,' he thought, 'although there can't be many people left that could see me.' Crossing several quiet streets and back-alleys, he walked up to the familiar building he lived in with Misato and Asuka. 'Well, and Pen-Pen,' he thought, remembering his guardian's pet, 'but she sent him to Tokyo-2 with Hikari.'

The building was one of the few that had been undamaged after the last few Angel attacks, something Shinji hadn't been grateful for until right then. 'It'll just be nice to be in a familiar hiding place,' he thought with a hint of humor. After riding the elevator, he approached the door to the apartment. 'I hope someone's home, I don't have a key,' he thought, mentally kicking himself for such an oversight. Stepping up to the door, his eyes went a little wide as he noticed the lock had been broken. Hand shaking, he reached out and slid the door open.

Walking into the dark of the hallway, Shinji could see that the living room had been ransacked. Moving about the apartment, he discovered the same had been done to the kitchen and two of the bedrooms. His room, oddly, had been spared. 'Probably nothing to find here,' he thought, remembering how little he owned. But his clothes, cello, and S-DAT player were missing…that was certainly strange. None but the cello were worth much, but it didn't look like they were stolen. Removing the raincoat, he closed the door to his room.

Returning to the living room, Shinji began to pace the small area. Possible scenarios played out in his head, not many of them very good. "Was there an evacuation?" he asked in the darkness, finally stopping his pacing. "D-did whoever tried to kill me get to them?" A soft click behind him shook the thoughts from his head.

"Shinji Ikari?" a man's voice asked.

Turning around, Shinji caught sight of a couple of Section Two agents. Neither one of them could've been older than twenty-one. And one of them was pointing a silenced handgun at the him. He nodded at them and spoke up. "W-what's this? Where's Major Katsuragi?" he asked, trying to hide the waver in his tone.

"We are unaware of the major's whereabouts at this time," the agent pointing his gun at Shinji answered. "Enough questions…we've been ordered to bring you back alive and…mostly unharmed."

"What? On whose orders?" Shinji asked, fear becoming a knot in his gut.

"Commander Ikari," the other agent replied.

"Father…" Shinji seethed under his breath, gritting his teeth and clenching his fists.

Upon Shinji's reaction, the agent with the gun spoke up. "Come on, you've got an appointment with the Commander."

The other agent walked behind the Third Child. As he began to put a pair of handcuffs on Shinji, the boy felt a strange instinctual urge course through him. In one swift motion, he quickly removed the cuffs from the agent and linked them on the man's wrists. And then made his point with a hard kick to the agent's chest, sending him sprawling across the floor.

As the other man began to react, Shinji made a grab for the man's arm. Two silenced shots came out, the barrel pointed down at the wood floor. The boy twisted the arm around and gave it a few sharp strikes, the handgun becoming lost from the agent's grip and onto the floor. The young man then used the leverage to bring a forearm down on the back of the agent's neck. He slumped to the living room floor, the fight having left him for now.

By now, the other agent had regained his footing and pulled his own gun. Shinji's attention quickly snapped back to him, diving behind the couch to avoid the shots. Counting off fifteen like it was ingrained, he quickly lunged out and for the gun he'd disarmed the other agent of. Taking quick aim, the Third Child shot the agent in both kneecaps and the arm holding the gun.

The agent fell to the ground in a heap, pain evident across his face. Rising from the floor and walking over to the man, Shinji kicked his gun down the hall. Stepping closer, he pointed the weapon at the agent's head. But as he was about to squeeze the trigger, his expression dropped upon realizing just what he'd done…the skills he'd just utilized. Skills he was certain he didn't have.

Shinji stood there, looking at his hands and the gun in one of them. Shaking and breathing heavily, he dropped the weapon and walked with unsteady footing towards the apartment's front door. 'Wh-what the hell did I just do?' he thought, a rush of adrenaline still surging through his frame. His thinking was cut off by a quick foot to his chin by an unseen third party. Upon regaining his senses, he looked at the person who has attacked him…any anger in his expression changed instantly to a mixture of shock and surprise upon seeing who it had been.

Standing over him was Rei Ayanami, the enigmatic First Child. She was clad in the same black plug suit he'd been wearing when Mathieu's ship had rescued him. And armed identically as the other two agents he had just dispatched. "Ikari," she spoke softly, the gun in her hand never wavering an inch as it was pointed at his face, "the Commander has need of you. Come along quietly…he said you were to be brought back alive. But if you persist, you will not be unharmed." Then, as if to make her point, she removed the gun's safety with a sharp click…

*****To be continued…*****

A/N: Okay then…one down, a few more to go. I figured it was time for something different (at least a little bit, for now) from me. And the idea had been with me for a month or so, so I figured it was time for another.

Who knows? Might keep this pace up and polish off a few more after this…

And, as promised last time…

*****Omake time!*****

We find the author seated at his computer, typing away at the last bit of this chapter.

Bard: Well…that's the first part down. (looking up at the room's newest occupant) Ah, so glad to see you all again!

Upon hearing those words, Mitsumi floats into the room and hugs the camera.

Mitsumi: (beaming) YAY! It's so nice to have you all back!

Bard: Ah…Mitsumi…

Realizing she'd been a little too glad to see the audience again, Mitsumi releases the camera and blushes slightly.

Mitsumi: (nervously) Oh, sorry about that. It's just that we haven't seen them in so long!

Bard: (sighing) I know, I know…

Mitsumi: (smirking) 'Bout time you got back to work, y'know?

Bard: (sweatdropping): Alright, I get it already!

Mitsumi: Oh, I just remembered something… (puts on her best mean look) I saw what you did in that other new one. You told me you weren't gonna do anything ecchi!

Bard: (sweating bullets) Ah…that. Well, at least I didn't get any more descriptive than-

Mitsumi: (cutting him off) THAT'S NOT THE POINT!

Bard: (incredulous) It isn't? I think it ended at being more "cute" than "hawt", agreed?

Mitsumi: (thinks it over for a moment) Okay…I'll give you that one. (a dreamy look comes over her face) It WAS really precious…

Bard: (smiling) Indeed, it was the proudest moment I've had being a fan of them.

Mitsumi: Really?

Bard: Yep.

Mitsumi: (trying her best Asuka impression) Then I guess I'll allow it…but nothing more than that. You even think about writing a le-

Bard: (cutting in) The thought never even crossed my mind.

Mitsumi: (rolling her eyes and floating out of the room) Baka author…

Bard: (sighs and slumps in his chair, then looks at the camera) Well, that doesn't mean I can't get to that level again, right?

Mitsumi: (from the other room) I HEARD THAT!

*****End Omake*****

Pre-read for this chapter was done by the team of Dark Machine, Eric Blair, gesser87, and JimmyWolk. Thanks, guys.

Small note: this chapter and all previous/following it were written around late June/early July last year. So a quick "sorry" to everyone who may have been waiting for something after TLaWR. Revisions and pre-reading can take quite a bit of time, it would seem…

For any of you who are new to the community, all of my older (2004-2006) works have undergone a small bit of tweaking (as of the 14th of June 2010). So go take a look, tell me what you think. And review! Even if it's not positive, review!

As usual: good comments will be appreciated, bad ones will be ignored (or kept for firewood). But I do favor good/helpful criticism, so send it my way!