I'm sorry about the end of chapter 1, I just realized that I lost the longer version with more narration.

Basically, Nagate and Tsumugi escaped the cave network as it crumble around them while being chased by our favorite gauna-shogouki. As the main gauna body get destroyed, its control on shogouki ended, and thus Shinji was released. The team took him back to Sidonia as a placenta sample.

I probably would re-insert this scene as a flashback sometime.

If you guys got some Eva X sidonia ideas that you want to share, please do so. I would like to hear what's in the mind of fellow fans; how to meld these two shows together.

…. ….. … ….

"Dr Yure, the analysis is complete. The specimen captured by Tanikaze are hundred percent human DNA, save for an unidentified red core in his abdomen."

Izana's grandmother stared at the screen. A gauna in the form of a young boy, like Hoshijiro, lies on the floor of the containment cell alone. He held his arms close and whimpered a little as if he was cold. She turned on the communicator inside the cell.

"Please respond if you can hear me?"

The naked boy woke up and rubbed his eyes. He scanned his surroundings, a room as big as a tennis court, well lit, with a wall of glass facing him. The floor is freezing his feet off.

"Yes, may I know where I am?"

Dr Yure froze for a second there, before turning to the lab analyst.

"Get me the commander, now," Yure ordered.

…. ….. … ….

A week later…

"Congratulations, Shinji, you have finished the puzzle with remaining time of eight seconds."

Shinji slumped to the floor, he didn't know he would be pleased to hear the sweet robotic voice telling him of his success.

"Why don't you show a little more spirit?" The robotic arm with finger tips of lightning got dangerously close to his forehead.

Shinji moved on his butt and pushed himself back to get some safety. Electric shock is a good teacher. "Yay," he faked.

"Here comes the reward." The lighting in the cell was powered down, then a spotlight in the center appeared. Another robotic arm came from the ceiling carrying a small case with it.

Shinji approached it cautiously, having being told of a reward many times earlier only to find that it was not. He pressed a green switch and compressed gas escaped from the case. Inside was his salvation from cold, a set of beige military uniform similar to what the Nerv crew used to wear. One problem, it was a female uniform. Between embarassment and having his butt frozen, it was not much choice.

He looked at the sports bra for a moment, then to the robot arm, back at the sports bra. It was cold anyway, Shinji reasoned. He continued putting on the rest of the uniform, with the miniskirt as the last piece.

In the science lab where the experiment was being held, Dr Yure walked in and saw the whole dressing scene.

"Whats with the female uniform?" She asked the analyst.

"Surplus stock, maam."

…. ….. … ….

Back at Lala's kitchen, the occupants crowded over the dining table with Yuhata in the middle. Nagate, Izana and Tsumugi had their attention on the holo screen broadcasted by Yuhata's communicator. They had watched the stream of the experiment carried out on the gauna specimen for a while now.

"This is cruel, don't you think so, Tanikaze?" Tsumugi prodded the only male in the house.

Before Nagate could answer, the commander's aide chided.

"We are doing it for science. It's done for the good of humanity." She giggled as the specimen who call himself Shinji got zapped again for performing badly in a test.

"He's kind of cute though."

Izana gave her a disapproving look.

"For a monster."

Now she find herself stuck between Tsumugi and Izana. She closed the screen and held her hands to surrender.

"Ok, enough voyeurism for a day. Lets get some food."

"Even if we may not be able to get any closer to communicating with the gauna's, we can still accept him as part of Sidonia, I hope. He looks like a decent guy to me. Besides, Tsumugi is proof that we can coexist peacefully," Tanikaze finally had his chance to speak.

"Tanikaze…" Tsumugi swooned.

Commotion could be heard outside the cafeteria. Nagate and friends, minus Tsumugi rushed out to check what it was all about. They found an unruly mob barging into the academy area carrying pickets, lead by a man with long blond hair carrying a loud speaker.

"Stop resisting us, we already have over fourty eight thousands signature. Before the night is over, we would have a representative to check on the welfare of our honored alien guest. And the world will know if the military has treated him with the full privilege of an ambassador of the Gauna race. "

"Hail our new alien overlord!" His followers chanted.

"You guys can't hold your rally here, it's a military zone!" The few guards who were severely outnumbered by the mob shouted back futilely. With less than a dozen of them against this crowd of five hundred at least, they don't want to escalate the situation.

"Open your eyes and see for yourself. Heaven has sent its messenger to us. Your days of fighting is over. We can finally walk hand in hand with our gauna overlords towards an era of everlasting peace. You don't have to serve those immortals; to do their selfish biddings anymore."

A senior figure among the guards stepped forward. "Shut it, Kensuke. We had captured placental specimen before this and you know of it. The gauna can copy the human form, and they are just repeating the process. This is no difference."

"Your immoral superior is just withholding information. Go forth and challenge them; does your latest gauna specimen not speak the language of human perfectly? Does he not practice manners just like a civilized human would be?"

The group of pro-Gauna activist got louder with various other accusation, from draconic laws forbidding specific acts of debauchery to lowering the requirement to get a law passed. The leader, Kensuke seems pleased with himself.

"Among the soldiers, they are those that stand with us, yet their voice silenced. Today we give them a reason to speak out."

He drove the crowd to a crescendo , but never actually uttering the word 'charge' himself. That would run afoul of some archaic seditious law. It was best to leave the dangerous acts to the mob while he grabbed the limelight. He smiled as his followers run pass the weak human fence made up by the military guards.

"Whoa, look at that group of hot pink haired clones. Let's get their signatures!"

Ren wind up her fist of death and put it through a tablet, not slowing down a bit, into the face of a slightly obese male activist. He fell onto the concrete; arms wide spread still holding tight to his electronic device and a stylus on another. His other co-activist stopped in their track, not knowing what to do next. If they approached the clone soldiers to retrieve their fallen, they might get their face stomped too.

"He walked into my fist, I didn't do anything. You all saw that right, sisters?"

Ren lead her group towards Nagate and his friends, taking the shortest path; right over the body of the fat activist. A dozen feet made cushion out of human flesh. The remaining activist made way for the Honoka sisters as they freely walked away.

"Hey, is that dude having an erection? What a deviant…" a grossed out activist pointed out.

Further away, Nagate found himself surrounded by a group of pro-gauna advocates, Izana and Yuhata stood by his side protecticely. They were calling him the number one alien, synthetics and transsexual sympathizer in Sidonia and wanted Nagate to be their poster boy in the military to support their cause.

"Who the hell are you calling a transsexual?!" Izana spun her 10 fingered hand into a drill.

"Sir Tanikaze, your support to our cause will bring us to new heights. Your relationship with our princess Tsumugi is what we tell our kids for bedtime stories, and for those without kids, we just bore the hell out of our relatives and friends with steamy tales of human and alien romance."

"Princess Tsumugi?" Tanikaze mumbled, the first time he ever heard this label given to his friend. He wanted to follow up with what sort of totally fictional story they were talking about him and Tsumugi.

"So if you would be so kind to help us out, and we utmost believe that you will, please just sign here."

The unshaven man with checkered shirt motioned his right hand, but it just wouldn't budge. He wasn't even aware that his wrist was locked tightly behind his back. He wanted to turn his body around only to find himself kissing the floor.

"Did you see how he tried to reach backwards and grope me?" Ren cheerfully said.

Izana and Yuhata stared in horror at the random act of violence. Maybe not Izana because she was used to punching Nagate through walls.

"There Nagate, a few more like this and we can call it even." Ren flipped her hair and propped one feet on the head of the pro-gauna guy.

"It's nothing, really." The only male pilot in the group rubbed the back of his head, counting his luck that he was not the target of asskicking this time.

…. ….. … ….

"What do you think Ochiai?"

Commander Kobayashi's bodyguard stepped toward to his master, floating in her luxurious personal chamber.

"The most likely scenario would be specimen Shinji being the gauna latest attempt at anti-human superweapon. Those monsters made the perfect human to date - to infiltrate our rank, using the sum memories of all humanity who was consumed, and altered it according to their needs. He appears cooperative right now, but once he gained our trust, he would reveal his true nature. "

"I asked for your opinion, not what I'm thinking," the commander replied, her tone was not of anger but amusement that her confidante would be so close to her thoughts.

"I'm very keen on Dr Yure's theory. Some other seedship or according to her even more far fetched story, another branch of human species took root on a far away planet. In their war against gauna, they developed this humanoid mecha based weapon specializing in close quarter combats. We don't know much about the gauna except for their weakneses to kabi, but we have determined that the gauna's are capable of information transfer.

My take is that gauna forces consumed this weapon and its pilot, possibly also named Shinji, and repurpose it to their end. Deploying the armored gauna in a cramped fighting space seems consistent with their ever improving tactics against our weapon.

On the aspect of developing a weaponized human, capable of communicating in our language and with a consistence memory, it's too huge a jump from what we have observed with placental Hoshijiro.

The lack of a standard true body, instead replaced with a red core, lend some weight to this theory. He could be a chimera developed by other seedship, although his story insist that he wasn't living in an advance space faring age. "

Ochiai paused for a moment.

"Yes, I would prefer to believe that our gauna specimen could be benevolent to Sidonia."

"Didn't know you're such a romantic. I want this thing fighting for me…for humanity cause. What of his relationship with the armored gauna?" Kobayashi floated down as the artificial light slowly dimmed.

Ochiai carefully dressed his master, his fingers deftly avoided touching parts which would be impolite.

"Dr Yure has no conclusive evidence yet due to the specimen's completely new biological construct. However, she believes that the red core is capable of energy to mass conversion. The specimen has withstood all physical stimuli without turning violent. Therefore she was lead to believe the trigger to be a psychological one."

…. ….. … ….

This was the third week Shinji stayed in his cell…

"So when can I get out from this cell? I have done all your test, answered all your questions. What else do you need from me?"Shinji asked the disembodied voice who had been his only companion for all his duration in the cell. He didn't even know how long he was here. He fell asleep for perhaps ten times, maybe a week plus he guessed.

"No Shinji, there is one last thing you need to do before you can meet me." The robot arm wagged a finger, her tone sinister.

"What can I do for you?" Shinji pleaded. Any extra time spent in the cell is slowly driving him insane.

"Listen carefully, the world you know of….has ceased to exist. The evil race of Gauna destroyed earth five thousand years ago. And you Shinji, is the last human survivor."

Shinji fell to his knees and screamed the classic. "Nooooo!"

"That's not true, you said you're a doctor and I should trust you. Wait, if I'm the last human survivor, why did you put me through all that torture test?"

"You got me. I'm not really a doctor. I'm just an artificial intelligence designed to keep the last human alive no matter the cost. Let's get back to business shall we? I need to retrieve a sperm sample."

The metal arm made a vertical grip with its fist and pumped it rapidly while slowly advancing toward Shinji's groin. The boy ran around the room while screaming "Gotta run away" repeatedly.

In the lab's control room, an analyst laughed maniacally as she operated a joystick to chase her experiment subject around. Her hand roamed the console looking for something fun to press, and she found one 'Phaser set to frag.'

A gloved hand caught her wrist before she can press it.

Dr Yure glared at the spectacled girl looking so small next to Ochiai. "What on earth are you doing?"

"Extracting sperm sample, maam?"

"We already have all the fluid analysis done two days ago."

"I was thinking, maybe if we extract it through the manual way. Then we let the juice get exposed to air and artificial sunlight, it could have a different result. This is gauna sperm we are talking about, it could turn into something super for all we know."

Yure eyed the badge on the girl. "Dr Taki, Phd in Hygiene Science. Sanitory Department."

"Ochiai, get her the hell out of here."

…. ….. … ….

In the research lab of Toha industry, Tanba slowly moved away from the very irate Sasaki who was arguing with Nagate regarding some customization. The old engineer waved his hand and shooed away other engineers in the area, leaving the two alone.

"Stop asking me to do the impossible already!"

"But captain Kobayashi said I can talk to you directly regarding customization."

She pointed at the holoscreen showing a particularly savage attack by the armored gauna launching a well executed round house kick to Tsumugi's head.

"That kick has equivalent destructive force of a meteorite-class mine. We don't have that technology to make such powerful actuator for Guardian limbs yet. And even if we did, the cost would be so exorbitant high that we would rather just up-armor all existing unit with megastructure plates."

"We already fought two gauna which excelled at close quarter combat. Who to say that we wouldn't encounter more of it. We need to be prepared," Nagate countered.

"And then what, all of you guys just drop your guns and start brawling with gaunas? Our strategy had always placed emphasize on long range weapons. The reason is that your average pilots, no matter how much time and resources we throw at them, they couldn't dodge a tentacle whiplash. Blowing so much resources on one unit so some guy could have a macho duel is a giant waste."

"I'm trying to save lives here."

"And whose life is that? Your girlfriend?"

Sasaki was shocked that such word could came off her mouth too. She really has to keep that temper in check. There are many things which couldn't be fixed with engineering expertise.

"Hey, why don't you go check out the simulator, we got some new melee weapon patched in. Just come back a week later, I might have something for you. It's not like I don't want to see gauna's getting their face caved in." Sasaki closed the conversation with a mellow tone.

Nagate thanked her, bowed slightly and left her lab. When the pilot left her sight, Sasaki's huge wrench ricochet across the wall only to fall to the lower deck hitting some poor souls.

…. ….. … ….

Note: If you read chapter 1 in its messy state, I'm sorry. I added the" … …"scene change. Still getting used to after such a long time.