Millennia ago, the Ancestral Race from the far distant world of Iscandar launched the Seeds of Life throughout the galaxies. Two Seeds landed upon the 3rd planet of the Sol System. The first to land contained the being that came to be known as the Angel Lilith, It wiped out a large number of life forms upon the planet, the First Impact, and she produced the Lilin, later known as Humanity. Unfortunately, a rare occurrence happened, and a second Seed of Life landed upon the planet Earth, this one containing the Angel Adam. Thousands of years passed by and the Lilin grew into a great race of nations, until they discovered the dormant second Seed of Life. Adam was awakened and the Second Impact began.

War broke out against the Children of Adam and the Children of Lilith, while some foolishly sought to ascend to another plane of existence. Under the guise of creating defenders to battle the Children of Adam, hybrid creations called Evangelions were produced, with the bodies of Children of Adam, but with the souls of Lilin, and piloted by human children connected to the souls bound to the Evas, a long conflict broke out between them. Among them was a youth named Shinji Ikari. Tormented by his father and those working for him from a young age he was reared to bring about the end of the world and the rise of Instrumentality. Through interaction by his fellow Eva Pilots and those around him, at the last moment, at the peak of the Third Impact, he saved the Lilin. One Third of the Human race rose from the result of the Final Impact, but the world was devastated. Oceans were either evaporated or replaced by primordial fluid known as LCL, cities were leveled, and plant and animal life were wiped out.

Six years has passed since Third Impact. Life on Earth is wearing thin and hope of survival fades by the day. But a new hope will soon rise from a relic of the past, manned by those who wish to redeem their actions…

NEON EXODUS YAMATO

"Seagull to Tokyo-4, Seagull to Tokyo-4. Supply pick up of food and distilled water from Hong Kong has fully loaded and we are in the air and in route. We will be arriving in ETA two to three hours, if all well. Over."

"Tokyo-4 Acknowledge and will have the welcome wagon out for you, Seagull, fly safe."

"Roger that, T-4, Seagull out." Toji Suzuhara put the radio microphone back in its place and glanced to his partner in the pilot seat of their air transport Seagull. "Well back to Japan, huh?"

"Haven't been to Tokyo-4 in a few years," Shinji Ikari shook his head, "I might make it a few hours without a tomato thrown at my face."

"Tomatoes are in rare supply, my brother!" Toji laughed as he leaned back, "They won't waste one on you."

Shinji gave him a small smile. They had been friends since his time on Tokyo-3, before the Impact. Toji was one of the few who came back after he halted the Impact to not reject him angrily. After a few years of traveling on his own, Shinji stumbled across his old friend again, and for the last two years they had transported supplies across the devastated wasteland that was once the beautiful Planet Earth.

"This is weird," Toji said, bringing Shinji out of his thoughts.

"What's wrong?" Shinji asked, noticing his friend, who was studying a long range radar.

"A lot of air transports are moving toward Tokyo-4," Toji said, pointing to the various dots and their projected trajectories. "We got a pretty packed load, too. Something's up."

"Whatever it is, we may find out when we get there," Shinji said, glancing back to the window.

"Right, right," Toji nodded, unsnapping his restraint belts, "I'm going to check the load. Don't do any loop-da-loops."

"Please," Shinji smirked, "I wouldn't want to damage the load." He said, and Toji shook his head and opened the back hatch of the cockpit.

Shinji watched him leave and close the hatch behind him, and as he turned he wasn't alone in the cockpit. In Toji's vacated seat was a young girl with pale skin, light blue hair and crimson eyes, wearing a blue and white school uniform.

"Ayanami?" Shinji blinked in surprise.

"In one year Humanity will end, Shinji," She said, turning her crimson eyes to him. "You and Pilot Sohryu will decide the fates. I am waiting for you, Shinji. But please, do not let them use our gifts as a weapon."

Shinji shook his head staring at the clone. "I don't understand, what are you talking about? You're dead… how… where are you waiting for me? What gifts? Is there going to be another Impact?"

"Yes," Ayanami began to fade, "its effects on Humanity will be yours and Pilot Sohryu's to decide."

Shinji gapped as the girl disappeared. He sat there for a moment before rubbing his face. "Shit…" He muttered to himself.

"You ok, Brother?" Toji asked as he reentered the cockpit.

"Toji… do you think Ayanami could have survived?" Shinji said, avoiding eye contact.

"You and your Eva ripped her and Tabris to pieces if memory serves," Toji said as he retook his seat, "Don't see how she could have made it, but then again, she was a resilient wall flower…" He gave his friend an odd look, "Weird dreams again?"

"Just… something popped in there," Shinji replied, tapping the side of his head.

Both young men's eyes widened when the Seagull jerked with an impact. "What was that?" Shinji asked, gripping the controls.

"We got trouble," Toji said, glancing out the window to see a group of dark colored aircraft fly past them. "Freight Pirates…"

"Haven't run into any of those for a while…" Shinji shook his head as he hit the throttle. "Seagull to any available aircraft! Mayday! We are being pursued by pirates. Request immediate assistance! Mayday! Mayday!"

"Take the stick," Shinji ordered, as he hit some switched bringing up the aircraft's defense guns controls.

"We don't have many rounds left, Shinji," Toji said, "Make every shot count, Shinji!"

While the fighters were more agile heavier armed, Shinji and Toji had the advantage that they didn't want to damage their supplies. Shinji closed one eye and focused his sights on one of their circling attackers. "Target locked, taking it out," Shinji growled as he pulled the triggers firing the aircraft's twin machine guns, and ate through the jet's wing armor. It exploded violently as it fell from the sky.

"One down, three to go!" Toji cheered, jerking the stick to dodge oncoming fire.

Shinji managed to get another in his sights and studied the fighter. "I think that one's the leader…" Shinji said, "Take it out and the others will probably bug out…"

"Then what are you waiting for?" Toji asked, moving the Seagull into firing position.

"Got the target… FIRING!" He pulled the trigger and only the sound of clicking echoed. "Oh crap."

"Should have splurged on ammo…" Toji closed his eyes, "Kensuke would kick our ass for this…"

"Don't worry," Shinji gulped, "I think these guys are going to do it for him…"

Shinji and Toji watched as the lead fighter turned and headed toward them, and then exploded violently. A new fighter flew through the exploding debris, this one far more advanced and painted completely red with the image of Evangelion Unit 02 painted upon the side of the jet. "It… can't be…"

"Civilian Transport," a very familiar voice with a German accent came through the radio. "This is Red Tiger Leader. We got your backs and going to escort you to T-4."

"C-Confirmed, As-Tiger Leader," Shinji replied, trying desperately to hide his voice. He failed.

"Ikari?!" Asuka Langley Sohryu's voice chimed back, sounding almost happy and excited. "Wow, I saved your ass… AGAIN! Just like old times!"

"Um… yeah, thanks, Asuka…" Shinji said awkwardly.

"You are VERY welcome, Third Child," the overtly confidant replied, taking position in front of the seagull. "Now be a good Baka, and follow me. And don't you dare try to run away from me again."

"Roger that," Shinji shook his head.

"I'm serious, Third," Asuka sounded honestly angry, "Even make me think you're going to break formation, I will blow your ass to smithereens! Red Tiger Leader out."

"I think she missed you," Toji smirked.

NEON EXODUS YAMATO

Chapter 1: Rising like a Phoenix

"How are the preparations, Captain?" the chairman of the barely functioning United Nations.

"Ship construction has been completed, Wave Motion Drive Engine has been tested and ready, and all weapon and defense systems are green. All we lack is loading enough food and water for our trip as well as getting the crew completely built up. I still lack my tactical officer and head pilot." The Captain replied.

"We don't have much time, just barely a couple days past a year before life on earth will be impossible," the chairman shook his head, "There are still many who do not trust you. And you cannot deny your hand in causing the Third Impact."

"I cannot, that's why this crew and I volunteered to do this," the Captain nodded, "We made this mess. We're cleaning it up."

"Very good, be ready to begin Operation Star Blazers as soon as you're fully prepared," the chairman nodded, "UN out."

"Hmm…" the Captain sat back in the captain's chair on the empty bridge and sighed loudly.

"Captain," a woman spoke over the com system.

"Report," the Captain said, glancing down at the blinking com light.

"Red Tigers are returning, Commander Sohryu said that she's bringing you a present," the woman replied.

"Oh boy… I'm on my way. Thanks, Maya," the Captain stood up and left the bridge.

-NEY-

"Keep close," Asuka instructed over the com as they flew over what was once the Pacific Ocean, still a few miles from where the Red Sea remained.

"We're not even headed toward Tokyo-4 anymore…" Toji said as Shinji maneuvered the Seagull behind Asuka's fighter.

The wing of aircrafts flew low and over what was once the ocean floor. "Would you look at that…" Toji said, and Shinji looked to see the wreckage of an old World War II battleship. "Kensuke would be going nuts if he saw that thing…"

"He'd love it," Shinji noted.

Asuka slowed down and Shinji backed off the throttle, and to the boys confusion twisted down into a canyon, on into a hidden cave. Once inside, the boys were surprised to see a fully furnished military complex. "Whoa…" Toji gapped, "Now this is awesome…"

"Transport Seagull, you are clear for landing on bay A-12," a woman's voice spoke through the com.

"That sounds like Ms. Ibuki…" Shinji blinked, before picking up the com mic. "Roger that, we're touching down eta two minutes…"

Shinji effortlessly brought his transport down to the landing pad, and the two boys walked down the gangplank. He blinked when he saw a beautiful young redhead in a red and yellow flight suit waiting for him with hands planted firmly on her hips.

"The Red Devil…" Toji recognized, then leaned over to Shinji and whispered, "She grew up nice…" his eyes admiring how the flight suit clung to her curves.

"Toji Suzuhara," She said power walking toward them. Then to Toji's terror, threw her arms around him in a friendly hug. "Good to see you aren't dead. Hikari would be sad… sorry how that worked out, too, by the way."

"Um… thanks… and good to see you too, Asuka…" Toji said awkwardly.

"And… You…" Asuka turned her eyes on Shinji with eyes of pure murder.

"Hey, Asuka, how have you been?" Shinji asked, and Asuka's skin flinched and twitched at the sound of his voice. He noticed she had a long, faded scar across her left eye, which contrasted her right ocean blue eye with an odd mix of green blue and red.

Before he could say anything else Asuka's clinched fist slammed into his chest just below his ribs. The air escaped his lungs, and as he tried to suck in another breath, her knee slammed up between his legs. He was finished off by a brutal upper cut that sent him spiraling to the ground. "YOU MISTSTUCK! She screamed as she towered over him, "DU HURENSOHN!"

"What was that for…" Shinji groaned, curling into a ball.

She stared at him in disbelief, "You have to ASK? Are you really that stupid? WHERE WERE YOU!? Not even a word! Not even a note! NOT A I HATE YOU, NOT A YOU SUCK, not even… a goodbye. You just took off in the middle of the night. And what? You expect me to just pull you in a hug, kiss your cheek, and tell you how much I missed you? FICK DICH, IKARI!" She yelled, then turned and stormed off.

"You ok, buddy?" Toji said, going down to one knee beside his friend.

"I… might… have had that coming…" Shinji groaned, forcing himself to a seated position.

"Look on the bright side," Toji patted his shoulder, "At least you know she hasn't changed much."

"Captain on Deck!" a dock worker called and everyone around stopped and stood at attention. Shinji and Toji glanced and spotted another familiar face, and much to Shinji's relief, Misato Katsuragi, dressed in a Captain's long coat and white and black navy captain's hat, looked happy to see him.

"Misato-san…" Shinji said as his old friend and former guardian walked toward him. "Please don't hit me…"

"What happened?" Misato asked as she offered him a hand.

"Asuka found me first…" Shinji groaned, accepting her hand. She flinched at the admission.

"In her defense, she did take your sudden disappearance rather hard…" She said as Shinji dusted himself off. Her eyes traveled across Shinji's body in a very un-parent-like way before she smiled at him. "You've grown up, Shinji." She said with a smile.

"Thanks, Misato…" He blinked in surprise when she pulled him into a warm hug.

"I've missed you, Shinji," She said, squeezing him slightly, "Welcome home."

"Where are we?" Shinji asked as they released one another. "What are you doing here?"

"I need to talk to you both about that actually," Misato said, "There was a purpose for your transport order beyond the shipment. Come with me and let's talk in private."

"I have a bad feeling about this, Chewie…" Toji whispered to Shinji.

Shinji scowled at his taller friend, "The hell I'm Chewie!"

Toji smiled and shook his head, "Who's the jerk with a heart of gold, and who's the straight man?"

Shinji blinked a moment before a look of disbelief and anguish crossed his features. "Shit… I am Chewie…"

They walked into a small office and Misato closed the door behind them. "Have a seat, boys," Misato said motioning to the desk as she walked around to the other side of it.

"I'm certain you both have noticed with your transporting all over the world… the Earth isn't getting better," She said, pressing a button on a keyboard on her side of the desk. A moment later a holographic image of the Earth and the Moon appeared. The Moon was still soaked in Lilith's blood while the earth, where it was once a beautiful shade of blue and green with several white clouds was now dark red and brown with a few small patches of blue and green. "The truth is the Earth is dying."

"All studies show that in just a little over one year's time the Earth will not be able to support human life, and short while later, no life whatsoever," She said as the green and blue faded away leaving only red brown and black.

Toji and Shinji stared in shock, Shinji more so as he remembered the warning Rei had gave him just a short while earlier. "There has to be something we can do, Misato…" Shinji said, looking up at her.

"How much do you two know about your world history?" Misato asked, pressing a few buttons, "Particularly World War II?"

"Studied it in school, at least until the world ended," Toji replied, "Then survival and pilot training kinda took precedence…"

"I'm certain you saw the wreckage of the battleship above this base?" Misato asked, and the young men nodded. "During World War II, the Imperial Japanese Navy built the largest and most heavily armed warship to ever travel the seas: The Yamato, the flagship of the Japanese Combined Fleet. Unfortunately, she didn't see that many battles. Most notably she defended Japan during the Battle of the Philippine Sea, and went down fighting during Operation Ten-Go." She explained as video footage of the WWII era Warship was displayed before them. "We've been working at repairing and refitting her here."

"No offence, Katsuragi-san," Toji said looking at the seagoing warship, "But there's not that much water left. A battleship, especially a big battleship, isn't really that useful anymore…"

"Oh, it does more than float now," Misato said, smiling and glancing between the young men, "Alright, Toji, I expect this to be all Greek to you, but Shinji, how much do you know about the moons, the black moon and the white moon?"

"Where the Angels originated from… in according to my Father and Dr. Akagi's mother us too," Shinji nodded, frowning as he didn't want to go back to that part of his life. Ever. Again.

"The question is, where did they come from?" Misato pressed some buttons and the earth reappeared and began to zoom out. "This is the Milky Way, we are here," She said and a little flashing arrow with a smiley face appeared on the halo-projection, "After extensive research using Evangelion technology and… other things we have learned that they come from what has been dubbed the Ancestral Race. For reasons we do not know they launched the Seeds of Life, the White and Black Moon, out into space… we have reason to believe that they were not the only two either. If they created this… technology that would produce Instrumentality then… we… believe that they have the technology to undo it."

"There is a way…" Shinji said looking at his lap.

"Excuse me?" Misato looked surprised.

"Misato, fool me once shame on me," Shinji glanced up at her, "Don't forget, I was in NERV, too. You know more than you let on. Rei came to you, too, didn't she?"

Misato ducked her head a moment, "We did get some… surprise intelligence as well as advice on how to properly use technology derived from NERV's Evangelion technology. Particularly something called the Wave Motion Drive."

"We have learned that Iscandar is here," Misato continued, showing a galaxy a great distance away from Earth. "It is estimate one hundred and sixty eight thousand light years away from us."

"It takes a year and a half for one of our ships to reach Mars at top speed, Misato… We'd… our grandkids would arrive there and their great grandkids would be making it back home," Shinji blanched at the map.

"That's where the Wave Motion technology is so… COOL!" Misato beamed, hitting some buttons. "While I have no idea how it works myself, that's more Ritsuko and the engineers' department, it has the ability open temporary folds in space/time. If we do fold jump after fold jump, including cool down times, we can be there in a less than a year's time."

"So we take a ship that has this Wave thing on it, find these Ant Siesta Race guys, find out how to undo the Impacts' damage, then come back home?" Toji asked.

"Yup, it's a glorified grocery run," Misato nodded. "I assembled the crew, majority of them are members of NERV. We all had a hand in leading the world to this kind of shape. Where the majority had no idea and was manipulated by Commander Ikari, all of our hands are still bloody regardless the motive. They… we see it as a way to redeem ourselves for our involvement. We have two more spots on my bridge crew needing to be filled: Pilot and Tactical officer/gunner. We need you both. I need you. Shinji, Toji, what do you say? Wanna go on an adventure?" She added with a smile.

-NEY-

"I can't believe she talked us into this…" Toji complained as they walked down the hallway, Shinji looking at a map of the base that Misato had left, with hand drawn instructions to Medical.

"You always said you wanted to be a hero like the Eva Pilots…" Shinji pointed out.

"Yeah, and that bright idea had me crippled till Third Impact," Toji grumbled, then stiffened in realization. "Sorry, brother. I didn't mean…"

"It's ok, and besides it shouldn't be that bad," Shinji shrugged, "glorified grocery run."

"We'll see," Toji said, and Shinji looked up at the Red Cross sign, "Here we are."

Toji opened the door and they walked into the med bay. A young brunette nurse turned and looked at them. Toji and the girl's eyes met, and Toji gapped and the girl smiled happily. "Onii-san, Shinji-kun, great to see you!"

"Sakura? What are you doing here?" Toji asked his younger sister.

"I'm one of Dr. Sado's RNs," Sakura Suzuhara replied, pulling out a blue rubber glove. "Captain Katsuragi gave us a heads up that you were coming. Now both of you… Drop your pants." She said, snapping a rubber glove on.

"Beg your pardon?" Toji asked while Shinji turned beat red.

"Drop. Your. Pants." She said slowly as if speaking to a child as she pulled a tray around.

"Why?" Shinji croaked, "If you don't mind us asking…"

"Couple reasons," She said, holding up a syringe, "Vaccination to the butt," And she held up a variety of probes and elongated Q-tips. "We have to test for any possible infections and diseases… all openings I'm afraid. Don't worry…" An almost sinister and predatory look crossed the young nurse's features. "I'll be gentle…"

-NEY-

Mars Base

"You're almost out of fuel, Kodai-kun," a blond headed woman in a yellow uniform said through the com from the command tower of the former SEELE now UN base on the surface of Mars.

"Have to make sure the asteroids are clear for the ship's course, Yuki-chan," the pilot of the shuttle said to his wife as he flew among the rocky debris.

"Going on a deep space mission to save all of humanity," Yuki said, somewhat dreamily, "It'd be amazing... Do think we'll ever have an opportunity like that, Kodai?"

"Maybe in another life," Kodai replied, doing a loop in his shuttle. "Never know, you might even be an ace-pilot!"

"I'm not that bad…" Yuki pouted. She blinked as the radar began to bleep in front of her. "Kodai, something's wrong…"

"I'm seeing it too, Yuki. As soon as I'm in and the landing bay is sealed, head toward the bunker…" He said, seeing the large beeps surrounded by hundreds of other beeps approaching from the opposite side of Mars from Earth.

"Kodai, please be careful… hurry to me." She said, as she forced her hands to not tremble as she readied the base automated defenses and ordered an evac to the Anti-Angel bunkers.

"I'm on the way in," He said punching the throttle, "This is Commander Susumu Kodai of Mars Base, we have multiple UFOs approaching from unknown space, request assistance."

"They're never going to make it…" Yuki said softly.

"Someone will… hang on, Yuki-chan… I love you…" Kodai said as he brought his shuttle in, praying for a miracle.

-NEY-

Battleship Yamato Site

"Who are they?" Misato frowned from her ready room, looking at the transmitted information from Mars Base.

"Unknown," the UN admiral replied, "Mars Base has limited defense, and the personnel have been moved to underground Anti-Angel bunkers. Project Star Blazer's Warp Drive can get you there in time to save them on the way the mission. It is on the course path outside of the galaxy… it just seems you'll have to leave earlier than expected. Are you prepared?"

"Yes but I was hoping for more system tests before we leave the planet…" Misato frowned. She sighed and sat back in her chair, "Well, we wondered if there was any other life besides us… this can't be a coincidence that as the LCL is close becoming its purest on Earth that these guys show up seemingly on the way here?"

"It's not unlikely that they could be LCL scavengers," the admiral replied.

"ET Ambulance chasers…" Misato shook his head, "We'll take off as soon as everyone's on board and at their stations. Katsuragi out." She said with a nod.

"God's speed, Katsuragi." The UN admiral replied as the screen turned off.

Misato took a deep breath and lifted her mic. "All hands, this is the Captain speaking. We have an emergency situation at Mars Station. We will lift off immediately and go to rescue the Mars Base staff. I know we expected one more night on earth to rest and prepare but that's just how the dice rolls. All hands battle stations. Primary Bridge Personnel to First Bridge, we've been preparing for this, people. It's time to show them what we're made of."

She released the call button, and sat it down. A moment later the alert siren sounded and she pressed a couple buttons on her chair, and it lowered through the floor toward the First Bridge.

Shinji and Toji ran down the hallway and Asuka turned a corner almost plowing into Shinji.

"Watch where you're going you… Baka?!" Asuka blanched.

"That's Commander Baka now," Shinji replied, "Get the Red Tigers in their cockpits and on standby,"

"Wha… who the hell do you think you are? Do you honestly think you can tell me what to do?!" Asuka's face turned blood red with anger.

"Misato made me Tactical Officer," Shinji said matter-of-factly, "So that's who the hell I think I am."

Asuka blinked several times before glaring, "Ok, fine. But I sure as hell am not going to salute you!"

They parted ways and Shinji and Toji arrived at the elevator that took them to the bridge. They walked off to the advanced space-cruiser-like bridge lay out.

"Welcome to the bridge, gentlemen," Misato said, fully into her old NERV Commander mode. "Shinji take the gunner position, Toji, take the helm." Shinji sat in the center of the ship while Toji sat to the far right.

The boys gave a quick salute and took their positions. Misato picked up a mic. "Chief Aida, are we ready to go?"

"Wave Motion Drive online and charged, waiting for the command to connect the fly wheels, Sir!" the familiar voice spoke through the con, causing Shinji and Toji to look at each other in surprise.

"Do it, Chief," She looked forward, "All hands prepare for lift off. Open the windows."

Shinji and Toji covered their eyes as an outer layer over the forward glass broke away, showing that they were in the command tower of the one sunken wreckage.

"Wait, we're flying into space in a sunken chunk of scrap?" Toji asked.

"That was just camouflage for the repair and star cruiser upgrades," the ship's AI, Analyzer, replied through the consoles.

"All systems ready to launch," Maya Ibuki announced from her station on the left of the bridge.

"Alright…" Misato nodded and sat back. "YAMATO HASSHIN!"

The buried engines screamed as the ground trembled from the force of the mighty warship began to rise through the rocky ground. The fake rusty metal broke away showing shimmering new alloy metal armor. The long warship had one large thruster and two smaller ones below it at the rear, a large central tower with two bridges and the captain's cabin at the top, and a missile tower attached to the back of it, had two large three cannon guns on the rear and three on the front, and multiple twin cannons along the center sides, and at the very bottom of the ship's hull was a third bridge. Finally an odd port was closed at the very tip of the ship. From the ashes of the WWII Battleship Yamato, the Space Battleship Yamato had risen.

"All systems running optimally," Ritsuko reported from the third bridge. "We are ready to activate warp system as soon as we pass the moon's orbit."

"Good. Steady as she goes, Mr. Suzuhara," Misato said as they rose higher and higher into the sky. "Hang on, Mars. Help is on the way…"

Uchuu Senkan Yamato!

Farewell, Earth!
The ship that is departing is
The Space Battleship Yamato!

It departs now to Iscandar

At the end of the cosmos, bearing its fate
"We will come back, no matter what it takes,"
Answer with a smile to the waving people!

Going far from the galaxy toward Iscandar
A faint gleam of hope
The Space Battleship Yamato!

Farewell, Earth! Farewell, beloved ones!
The Space Battleship Yamato!
Bearing the fate of saviors of Earth
The men fight and the romance burns high
Somebody has got to do this
We are the people they count on…

Going far from the galaxy toward Iscandar
A faint gleam of hope
The Space Battleship Yamato!

The Space Battleship Yamato!

TO BE CONTINUED…

Next chapter: The Yamato's maiden flight faces a new threat. What secrets do these aliens hold? What secrets does the Yamato itself hold? Questions will be answered and questioned will be asked… as well as a good dose of fanservice! Neon Exodus Yamato chapter 2… coming soon!

Song credit: "Space Battleship Yamato" main theme (English translation)