Warning: While the base of this story will remain the same, it is currently being re-written. So be aware that all chapters will be changed/improved somewhat in the future.

A/N: I've had this idea for a while now and I'm glad that I've finally found a way to make it work.

While this is mostly an Evangelion story, I will be touching lightly into the Negima timeline. I say timeline since Evangelion takes place in 2015.

Amateur at work, so please don't expect a high quality novel.

Incantations and Bio-Mechs

Chapter One

A tener puer incompertus fortuna

(A young boy's unknown fate)

Calendar year 2005…

The train station. The last place a child expects to be standing shortly after his own birthday. But there he was, Shinji Ikari, waiting to be picked up by his uncle after a hard year of living without his mother and being alone with his cold father. With tears still fresh in his eyes and sobs still coming out of his mouth, he was unaware of the group of people quickly forming just around the other side of the building.

This wasn't an ordinary group of passers by though. Each individual was there for one particular reason; to get their hands on Shinji Ikari. What was it about this boy that attracted them to him? It has been said that after Third Impact, a child would be born with the power to choose the fate of the world. Furthermore, that this child was the descendent of both powerful warriors and wise leaders. That this apparent lineage is said to allow the boy to become anything he sets his mind to. Despite his supposed power, he will always return to his birthplace to either save or destroy humanity. With a child that influential, anybody would like to take him under their wing and show the world that their way was the true path.

Looking around the crowd you would see a lot of unique faces and equally unique plans for the young boy. The biggest problem among them though, is deciding who gets him.

"He needs to become a vampire and suck the blood of his enemies." A pale skinned and sharp fanged man spoke up.

"No, he shall become my servant and learn to please women in all forms." A female dressed in bondage gear, holding a whip, shouted and cracked said whip.

"He needs to move to America and learn the American way" A blond man with a scar on his cheek yelled. Everybody stared at him then laughed.

"He will become a Russian spy and be an irresistible ladies man."

"A lazy fan fiction writer."

"He will assist my grandson in managing my all girls dorm while I look for hot springs around the world." A short old women said quietly.

"A race car driver with no sense of morals."

"He will fight for our rebellion and become a stone cold killer with an addiction to pocky."

"An emo kid who likes to slit his wrists."

"He shall learn the ways of the force." A bearded man in a cloak calmly said as he waved his hand over the crowd.

"No! He will learn the way of the Sith, Jedi scum." An equally bearded man wearing a similar, albeit black, cloak shouted back.

While the still growing group of, mostly, people argued, a pair of mischievous blue eyes watched from the sky. Floating high in mid air was a small girl with a maroon colored school uniform and a black cape. She looked to be about ten years old and was clearly European. She flipped back her long golden blond hair and simply laughed at the sight below her.

"Pathetic." She chuckled. "I'll admit that some of them are close, but they don't understand what true power really is." She tapped the earpiece in her right ear, activating the device. "Chachamaru, I will be home sooner than expected."

"Understood, master. Dean Konoe will be pleased to hear that you are returning to campus so soon" The monotone voice of her Minstra Magi, Chachamaru Karakuri, answered back.

The young blond girl cracked her knuckles and then put up her right hand. She then began channeling her magic. "Lic lac la lac lilac" The group of people below heard the odd words being said and looked up to find a young girl floating in the air with a ball of violet colored energy swirling in her right hand. "Evigenato Taionion Elebos" She put her two hands together "Haionie Krystale" The ball of energy shot towards the shocked group. As soon as it hit the ground the entire group was frozen in place like they were just sprayed with liquid nitrogen "Be grateful I don't finish the spell or you would lose more than just the boy."

She turned her attention to the boy who was oblivious to what had just occurred, thanks to his SDAT and the headphones over his ears. Landing gracefully on the ground, the girls' cape flew off of her back and burst into dozens of squealing bats. Straightening out her uniform the girl then started walking up to the young boy. She stood right in front of him but he was still so upset and crying that he failed to notice her. People that knew this girl knew that she wasn't a very patient person. As a small vein began popping on her forehead at being ignored and she yanked off his headphones, startling him.

"Common kid you're coming with me." She grabbed his arm but he quickly pulled back and got out of her grip.

"Wh…who are you and wh…what do you w-want" Shinji asked, slightly scared of the girl who was clearly older and bigger then he was. She gave out a slight sigh but answered him because she needed his cooperation or the years to come would not go smoothly.

"My name is Evangeline Athanasia Katherine McDowell but it would wise of you to call me Eva." She gave the boy a formal bow. "And as for my reason to being here." Eva looked into his eyes "I have come to pick you up."

"Umm…hi…Eva…uh…actually I'm supposed to wait here…for my uncle…and I'm not…" he didn't get to finish as he was interrupted.

"Don't worry boy. I already discussed it with your uncle and he has agreed for you to come along with me." She obviously lied to him and then put out her hand.

"Uh…okay." The young boy timidly grabbed her hand. He may be smart for his age but he's still too young to see through her lie.

"Now don't freak out, boy." She warned him "La Lac Spiritus" Evangeline snapped her fingers.

"Why would…" The two children vanished in a flash of violet light.

In a little log cabin in a highly dense forest a strange girl, with antennae on her head, looking to be about fifteen years old prepared some tea for her masters' arrival. The girl was surprisingly tall for her apparent age and was currently dressed in a maid uniform. Detecting a disturbance she looked up to see a quick flash of violet light.

"…I freak out?" The boy paused for a moment "ahhh" Shinji freaked out as he realized that he was no longer at the train station and was in a strange house. Quickly letting go of Evangeline, he backpedaled against the wall "How did we…we were just…oh boy…I need new underwear." Evangeline let out an annoyed sigh and crossed her arms.

"I told you not to freak out." She walked towards the tall girl holding a tray with a small cup on it.

"Welcome home, master." The tall girl said as she handed Evangeline her tea.

"Thank you Chachamaru and could you please get the boy a change of clothes." Eva sat down in a chair, obviously made for a person much bigger then herself, and sipped her tea.

"Yes master." Chachamaru bowed and looked at Shinji "You shall come with me. I will assist you in acquiring new clothes." Though Shinji was still confused on what was going on the young boy felt surprisingly comfortable around this calm girl.

"Okay…Chachamaru, that was your name right?" He asked.

"Affirmative, Shinji Ikari." She answered back with a small smile.

After getting a spare pair of underwear, the two walked into a small city. He was clearly still in Japan but this place was definitely somewhere new to him. There were plenty of small shops available and the city was bustling with people. You couldn't tell that Second Impact had occurred when you were in this place but since Shinji was still so young he thought nothing of it.

After about ten minutes of walking they came across a clothing store. Shinji walked in but was unsure of what to get. He had always let his mother get his clothes.

"Come along." Chachamaru said as she lightly grabbed his hand and had him follow her. "I have the current data on your sizes and the styles most commonly used by your age group".

'That was a weird thing to say.' The young boy thought "umm sure." As he thought more about it, this girl was quite an odd one. She had long neon green hair and covering her ears appeared to be antenna of some kind. The way she talked was odd too…like she wasn't…human. Shaking those thoughts aside, Shinji followed her.

"Fancy meeting you here Chachamaru." A boy's voice came from behind the two. Standing before them were three girls and a single boy. The girls were obviously in high school but the boy looked to still be in junior high.

"Good evening Professor Springfield, Ms. Konoe, Sakurazaki-san, Asuna. She greeted the group. Shinji stared at the girls. Each of them was quite beautiful in their own ways and they all seemed to be standing awfully close to the smaller boy.

"So what brings you here Chachamaru?" The boy, whom she called Professor Springfield asked.

"I have come to acquire clothes for Evangeline's new apprentice." It was at that statement that the group finally noticed the little boy standing shyly behind Chachamaru, clinging to her leg.

'So, this is the child old man Konoe told me about, I sense lots of potential in this one.' The teenaged professor thought then kneeled down and said, "Hello there. My name is Negi Springfield. What's your name lad?"

"Ikari…Shinji Ikari." The boy stated timidly.

'Ikari…isn't that? Oh yeah, lots of history under that name.' The young professor thought, "Well Mr. Ikari, I have an idea. How about you and I get your clothes while the girls go and shop."

"That is an excellent suggestion Professor Springfield. You are more suited then I to acquire his new garments. I shall leave him in your care then." Chachamaru turned to leave with the other girls.

"But Negi-kun." The girl in the middle, known as Konoka Konoe, whined, "You promised that you were going to help us pick out bathing suits." Negi always seemed to get into these predicaments and had learned ways out of them.

"I'm sure Setsuna wouldn't mind helping you choose a nice one, Konoka." Negi said with grin.

"Negi-sensei." The girl in question, Setsuna Sakurazaki, cried out in embarrassment, blushing like crazy.

"Negi-bozu." The tall red headed girl with bells in her hair named Asuna Kagurazaka spoke up "Will you stop teasing Setsuna, that's my job you little brat." She berated him playfully.

"Right, right. Well Shinji, shall we be on our way?" Negi looked down at the boy.

"Uh yeah" Shinji said it just so he wouldn't be around so many people anymore. He was still getting used to big crowds.

Negi put his hand behind Shinji's back and began pushing him towards the males' section of the store.

"So you're Eva's apprentice in magic huh?" Negi asked.

"I…I guess…I don't really know what's going on." Shinji was just confused with what he's seen so far. Though he was young, Shinji still wasn't sure if he believed in magic or not.

"Well whatever it is." Negi spoke up. "I'm sure Evangeline will take good care of you." Shinji gave him a strange look. From what Shinji had seen so far he figured Evangeline to be a mean and uncaring person…like his father. Noticing Shinji's look of disbelief, Negi decided to explain a little more.

"Don't let her actions or words fool you, Shinji. Eva is a really nice and dependable person…she just takes a little getting used too. She's a bit rough around the edges you might say, but in the end, she's one of the good guys." Shinji just nodded his head. Maybe being an apprentice wouldn't be that bad. Shinji just had one thing left to ask Negi.

"I guess living with her won't be too bad but…I'm confused" Negi nodded and Shinji continued, "What's an apprentice?" Negi tripped over his own feet. Oh the joys of a conversation with a, just turned four year old, child.

Calendar year 2010…

"Sageta Magica Levitos" Shinji cast his lightning arrow spell...but nothing happened.

"Sometimes I truly wonder if you actually pay attention to us, boya," Evangeline said as she smacked him in the back of the head. The nine-year-old Shinji rubbed his head and looked over at Negi.

"I hate to agree with Eva…" The blond gave him a dirty look. "…but she has a point Shinji."

"Yeah, yeah" Shinji muttered as he turned away.

"You know you act just like her sometimes." Negi pointed out, eliciting a shiver from the boy.

"Don't even joke about that." Shinji grimaced.

"Then pay attention this time." Shinji nodded with a sigh. "It goes Sagitta Magica Levitas. You think you got it" Shinji nodded once again. "Well then what are you waiting for? Eva to smack you again."

"Actually, I kinda like it when she does it." Shinji joked while Negi gave him an odd look "Sagitta Magica Levitas" seven arrows of lightning shot from Shinji's hand. Standing in the background, still looking at her young apprentice, Eva commented to herself with a slight, but still out of character, smile.

"That's the way boya. You're developing faster than I would have imagined".

Calendar year 2015…sitting in Unit 01…

"So I just think it and it does it?" Shinji asked Doctor Ritsuko Akagi.

"Pretty much." She answered "You really should focus more on walking right now."

"Whatever you say." Shinji put his energy into walking.

"Maya, how's his sync ratio." Ritsuko asked.

"He's currently at a steady forty two percent. There is some interference though." The brown haired computer tech answered.

"It's that damn stick he's carrying with him." Ritsuko was a little angry that he wouldn't leave it behind.

"It's a staff." Shinji interrupted as Unit 01 took its first step "And I don't go anywhere without it." Shinji argued with the doctor, causing Maya to chuckle lightly.

"It's bad enough he took his 'staff' into the entry plug, but did he have to leave this little doll here with us too? It's giving me the creeps." Ritsuko looked down at the green haired puppet that Shinji had on his shoulder as he entered Nerv. If Ritsuko were to have looked closer she would have seen the dolls eyebrow twitching. Maya chuckled again as she noticed the twitch.

"Give the kid a break Ritsuko." Misato cut in. "He's activated Unit 01 and is already walking." The blond doctor let out a breath she didn't know she was holding.

"Fine but… don't let us down okay Shinji" Ritsuko gave up and decided to let fate run its course.

"Sure thing." The boy said as the angel advanced to his position.

"Where did we pick up Ikari's kid again?" Ritsuko asked.

"I got him up from Mahora Academy. Apparently he was under some kind of special education program." Misato told her. The two women failed to notice Maya smile at the name of Mahora Academy.

'Oh yes.' Maya thought. 'A very special program' the young tech knew a whole lot about Mahora since she went to school there from elementary all the way through college. Not only that, but Maya happened to have had a very special professor by the name of Negi Springfield. It was also at that time that Shinji had shown up at the school. She still remembers the little boy being mentored by Negi-sensei and Evangeline. She frowned a little as she thought of Eva. She got up from her seat and picked up the green haired doll Shinji had brought with him, then sat back down. 'Best to keep her away from them, for their own safety.' Maya was brought out of her thoughts by Shinji's screaming voice.

"Ahhh!" Shinji wailed.

"Relax Shinji…it's not your real arm." Ritsuko tried to calm the boy down.

"Are you seriously telling me that? Regardless if it's my real arm…" Shinji's voice hitched in pain "…it still freaking feels like it." Trying to compose himself, Shinji took a slow and deep breath. The fact that he was breathing LCL didn't help his situation. "I need to calm down, this is nothing. I've been in worse conditions before." The command crew didn't know if they should be relived at that statement or horrified. 'I might be able to fix this thing.' Over the communicators the command crew heard Shinji mumbling some strange words but Maya knew exactly what he was doing.

"Levitas Mico Ex Intus" Shinji chanted the key to unlocking his powers. "Penitus Vox, vigoratus meus socius vulnus quod fulcio suum animus" Shinji seemed to pulse for a second before his own magically energy began to flow out of him and through his entry plug. As the angel, Sachiel, picked up the damaged Unit 01 by its head, the angel noticed a strange surge of unusual energy begin to emanate around its foe and let go of the Evangelion instinctively. The flow of energy swirled all around Unit 01's body. "Now." Shinji whispered "Lets finish this."

"Ma'am." Maya shouted out. "Unit 01 is regenerating."

"What? How is that possible?" Ritsuko looked at the data but couldn't figure it out.

"His sync ratio is currently at sixty four percent".

Misato simply watched the screen with a small smile as Unit 01 tore apart the angel. The third angel tried to retaliate but it was silenced with a piece of its own body sticking into its core.

"The angel has, has been defeated." Shigeru announced.

"Great work Shinji." Misato congratulated the boy.

"Yeah…hurray…for me." Shinji passed out as he gave a victory sign to the monitor.

"Shinji?….What happened to him?" Misato shouted at Ritsuko.

"I'm not too sure." The faux blond replied "His vitals are stable; I think he's just exhausted."

Shinji woke up in a pure white room. He immediately recognized it as a hospital room from the bland white walls and the heart monitor.

"Why do I get the odd feeling that I'm going to eventually hate this particular ceiling?" Shinji mumbled as he sat up and felt a slightly painful numbing sensation in his left arm and instinctively rubbed it.

"Do not worry about the pain," A soft voice said, "It will go away in a couple days." Shinji looked to his left to see the blue haired girl that was almost forced to pilot Unit 01 with near fatal injuries. Upon further inspection he thought she looked quite cute with her short azure colored hair and crimson eyes; something he had grown accustomed to in his experiences at Mahora and the magic world. She still had the bandages wrapped around her head and left eye and Shinji once again felt some kind of unique, and slightly familiar, energy flowing from within her. Rei had noticed him staring at her and unconsciously blushed, which made Shinji smile. "…I…I must go now." Rei stuttered as she quickly closed the book she had been reading and grabbed her school bag. Rei has been known to never stutter nor pause. So when she did both the enigmatic girl immediately felt uncomfortable and left the room, confused as to why she acted the way she did and why she was even in Ikari's room in the first place.

"She's an odd one, isn't she master." A small voice said to his right. Looking up at the little table next to him he spotted the creepy green haired doll he had brought with him.

"You're one to talk, Chachazero." Shinji yawned as the doll stood up and jumped onto his lap.

"I'm not odd…I'm unique…not to mention adorable." The doll defended herself cutely.

"Hah, you're a demented, bloodthirsty, perverted, egotistical…" Shinji yawned once again.

"It's been a whole day and you're still tired?" The psychotic puppet asked with a bit of concern.

"It took a lot of my energy to heal that creature I was piloting. I barely had any energy left to fight."

"Well at least you beat it. I'm sure Eva would have been upset with you, had you of lost".

"What's with calling her Eva and not master?" Shinji thought it was weird for Chachazero to address Evangeline that way.

"She is no longer my master. I'm your familiar now, master, not hers."

"Fair enough. So, did you meet up with Maya?" Chachazero didn't get a chance to answer as Shinji's door opened. The green haired puppet quickly collapsed into his lap as Misato walked in.

"How are you feeling?" The captain asked as she closed the door.

"Like I got hit by a car…then a bus." He joked.

"Well, at least you sound okay." She laughed. "The doctors told me you could be released tonight if you woke up and well…you did" She took a deep breath "I also heard that you would be living alone in a Nerv sanctioned apartment and I thought that if you wanted to you could um…live with me instead. I just figured you might not want to live alone…that's all." Shinji thought about it for a second and let a small smile escape his lips.

"I'd like that captain." He answered.

"Please, call me Misato." She smiled back.

A/N: For those that wish to know, Shinji's specialty is lightning magic, but he is incredibly flexible considering his teachers.

I'm going to use as much Latin as possible but remember that most of it is literal and will seem a bit off if you actually understand Latin.

Because this is a Negima crossover, this story will have a Shinji x Harem pairing.

Read my profile and you'll see what I've got planned as well as details on my current projects. (Shameless plug, I know)

Review if you want to, but feedback is always appreciated.

Read ya Later.