Criminal Masterminds

Summary: Gendo left Shinji with a teacher. If only he had known what he was doing. Now, Gendo had a bigger problem to deal with: someone who can and will outthink him. Crossover.

Chapter 1: Secret Under Tokyo-3

"Sorry. Due to an emergency, all lines are down. Have a nice day."

Shinji Ikari sighed, hanging up the phone. He heard his Sensei chuckle behind him, "I never did like those things."

"Considering the lack of cell phone service, it was worth a shot," Shinji shrugged.

His Sensei scowled, "Indeed. I intend to speak to our service provider about it."

Inwardly, Shinji shuddered. His Sensei was not a man to cross. While he was only 5'6, a half inch shorter than Shinji, his Sensei was incredibly strong. While he never said who, his Sensei had told him that he had studied under the third greatest martial artist in the world. Combine that with his Sensei's trademark suit, black reflective sunglasses, pale skin, jet black hair, Domovoi, and his Sensei's IQ, and you have someone who could do a great deal of damage physically and psychologically.

There was also the fact that his guardians seemed to be hiding something from him. After all, his Sensei's wife, Kaa-san, didn't look like a normal human either. Her red hair was always covering her ears, and while she was 4'2 and obviously a full grown woman, her face seemed to be more like that of a child.

Still, they were his family. Apparently, they knew his mother as well, and had told him plenty of stories. The stories they told made him feel proud to be her son. He wanted to be like his mother someday.

The roar of helicopters pulled Shinji from his musing as he looked up, watching them as they soared towards the main buildings of Tokyo-3, unleashing their weapons at something within. That something emerged, black, green, a skull-like face, clawed hands, and stood almost 150 ft. Its eye sockets flashed, and a blast of energy tore through the helicopters like tissue paper.

"Did the commanders of those poor souls try to contact that thing before shooting at it?" his Sensei mused aloud. Beside him, his wife began to shake. He turned to her, "Are you all right, Holly?"

"I'm fine, Artemis," she replied. "That thing just brings back a few bad nightmares."

There was an explosion as another chopper burst into flames, the wreckage flying straight for them. Underneath his sunglasses, Artemis Fowl the Second's eyes flashed, briefly glowing blue. The burning wreck struck a blue wall of energy in front of them, and clattered to the ground. "That was unexpected," he said casually.

Shinji didn't understand how his Sensei could be so calm about it, and instantly began scanning for the source of the field that had just protected them. He couldn't see anything that would generate any type of force field anywhere, but he did see something else.

It was a girl. Her skin was pale, her eyes a deep red, and her hair a light blue. She was wearing a school uniform, and looked as if she were sad. As he stared, Shinji realized that he wasn't actually seeing a girl, as he could see through her. Was it a projection of some sort?

The sound of screeching tires made the three of them turn towards the approaching car that skidded to a stop in front of them. A purple haired woman poked her head out of the window, "Sorry I'm late! Which one of you is Shinji Ikari?" Shinji raised his hand. "Get in!" When all three of them approached, she shook her head, "No. No. I can only take Shinji. Those were my instructions."

Shinji looked at his Sensei. Artemis shook his head and turned to the woman, "I'm sorry, Miss Katsuragi. If you want to take Shinji anywhere, you will have to take me and my wife with you. We are his guardians. We know his father wants him here for a reason, but we have reason to not trust him. Whatever Mr. Rokubungi wants to say to Shinji, he can say to us too."

"I can't," the woman protested. "My instructions are very specific Mr. and Mrs. Fowl."

Smiling, Holly stepped forward, locking eyes with the woman. "We understand, Miss Katsuragi, but there are more important things right now," she said, and then began drawing on her magic. "Forget about your orders. We don't have time."

Mesmerized, she nodded, "We don't have time for this. Everyone get in. Hurry!"

Shinji took the passenger seat, while his guardians took the back. The second they were buckled, the driver hit the gas and they peeled away.

"Reminds me of Mulch," Artemis whispered to Holly.

Tears sprang to the elf's eyes unwillingly as she nodded in agreement. After she had chosen to marry Artemis, things had become shaky between her and the rest of the Lower Elements. Some said that she was more than a hero, but one who was showing the way to the reconciliation of Fairies and Humans. Others branded her as a traitor. In the controversy, she was honorably released from her service in the LEP, or Lower Elements Police, but was able to maintain contact with her friends in Haven. Mulch, Dooda Day, Foaly, and Trouble often spoke with her, sometimes asking for both Artemis' and her help on cases.

Then Second Impact occurred, and for all Holly knew, Haven was destroyed in the destruction that was unleashed. Within hours of the devastating event, all contact she or Artemis had with the Lower Elements was gone.

She felt Artemis' arm wrap around her shoulders as he whispered, "Sorry, I didn't mean to bring up any painful memories."

"Nothing painful," she whispered back. "Just remembering the good old days, and you're right. Miss Katsuragi's driving does remind me of Mulch. Remember when we found out he was our limo driver at our reception?"

"I seem to recall you telling him that if he wrecked the limo or went over the speed limit, you'd knock him out, and then give him a long, thorough bath," Artemis chuckled. Holly smiled back.

Shinji, who was watching out the window and studying the battle between the army and the creature, frowned. Why were they all backing away? Were they giving up?

No! They were…!

"Everybody Out Of The Car! Now!"

Screeching to a stop, Miss Katsuragi glared at him, before realizing what he was talking about. "No Time! Just Brace Yourselves!"

BRROOOOOOMMMMMBBBBBB!

As the explosion of the N2 mine sent out a shock wave that flipped the car end over end, Shinji gripped his seat, and began a mental exercise to stay calm. A squared plus B squared equals approximately C squared. If I have a right triangle with one side equal to 7 inches, and another equal to 10.5 inches, than 49 plus 110.25 is 159.25, and the square root of that is…

THUMP!

The car landed, breaking him out of his thoughts. He heard his Sensei mutter, "Ride's over. Everybody out." Shaking his head, Shinji realized that the car had landed on its top. Hearing a moan, he turned to see that Miss Katsuragi had blood dripping slowly from her forehead. Looking around, he realized that her binder that she had between the seats had struck her when the car flipped over.

"Miss Katsuragi, stay with me," he said to her. "Stay focused on my voice." The last thing they needed was for the one woman who knew what was going on to go unconscious on them.

After climbing out themselves, Artemis and Holly carefully extracted the woman. While they tended to her, Shinji climbed out of the car as well. He looked toward the creature, now sagging and partially melted. It was obviously still alive, but it seemed that the army had exhausted its resources.

While Shinji wasn't looking, Holly put her finger on the woman's forehead. Several tiny blue sparks traveled down her finger and into Miss Katsuragi's head. The magic targeted her minor concussion, healing it without anyone but Artemis and Holly knowing it was there.

"Are you all right, Miss Katsuragi?" Artemis asked as the eyes of said woman flickered.

"Misato," she replied. "M' name's Misato."

"She's still out of it a little bit," Holly said. "I don't think we can stop her from going unconscious."

Sighing, Artemis removed his sunglasses and began to focus. He turned Misato's head towards him, locking her gaze with his as the white's of his eyes began to turn blue. "Focus for a few seconds, Misato," he said, his voice layered with magic. "Where were you taking Shinji?"

"NERV," she replied.

"Why?"

"I don't know. His dad wanted him."

"What is NERV?"

"A private, secret organization funded by the UN to stop the Angels."

"And what are the Angels?"

"There's one over there." Misato's eyes rolled back and she fell unconscious.

"It looks like the creature is regenerating," Shinji said as he continued to watch it. "The N2 mine destroyed 35 percent of its body mass, and at the rate its regenerating, I'd say we have 2 – 4 hours before it begins to move again." He turned to see his guardians caring for their driver, and walked over. "Will Miss. Katsuragi be all right?"

"She'll be fine," Artemis said, checking his sunglasses for dust before putting them back on. "Her car looks mostly fine as well, though it's obvious the battery fell out, considering it's all over the street. Shinji, go into that store there. Get a battery, a blanket, some ice, and some bandaging wrap while Holly and I right this vehicle."

"That's stealing, Artemis," Holly protested.

"We have an emergency here, Holly," he replied. "However, if it will make you feel any better, you can write down the address, and I'll send them a check for compensation."

Holly nodded. That sounded fair enough. Shinji hurried off, and the second he was gone, Artemis turned his concentration to the vehicle. His blue energy field reappeared, picked the vehicle up, and righted it on its tires. Releasing the magic, he took a few breaths. "Are you all right?" Holly asked.

He nodded, "I'm fine. That just takes a lot of magic to do. I'm almost out."

"Save the rest," she told him. He nodded once more and then stood and opened the car. He began to rummage through the passenger side compartment. Holly was confused, "What are you doing?"

"Misato mentioned a secret organization funded by the UN, obviously some type of private army," he explained. "Obviously, if it was secret, she wouldn't know unless she was a member. Judging by her lateness, she probably looses track of time and location, so…" He closed the box, smiling as he turned to show several pamphlets that he had removed, "…she keeps a few pamphlets and maps around just in case."

Holly couldn't help but smile, "I love you."

At that time, Shinji had finished gathering what he was asked to get, and had returned. They put Misato in the car, covering her with the blanket, and wrapped her head up. While Shinji wasn't looking, Holly put a few more healing sparks into the woman for good measure. She sat in back to keep watch over her while Shinji began to unfold some of the maps in the passenger seat. Artemis installed the battery and took the wheel, driving more carefully than Misato had been.

It took them a while, but they managed to find an entrance to the Geofront under the city and arrive at the pyramid that bore the NERV logo. They met up with a doctor named Ritsuko Akagi and explained the situation. Misato was wheeled to the hospital ward, while Ritsuko escorted the others to an elevator, taking them further down.

"Does it feel good to be home?" Artemis asked Holly.

"The surface was always home to me," she replied.

"Funny," he chuckled. "You always said you missed being underground."

"Don't play mind games with me, Fowl. I'm not in the mood for them."

"Oh, yes you are, Captain. Otherwise, you would have stayed silent. However, you do have a point, so I apologize."

Holly sighed, "Sometimes, Fowl, I think I liked you better when you were a brat."

"And sometimes I think that I liked you better when you had a gun pointed my direction."

"I can fix that."

"So can I."

"Try it. I dare you."

They kissed passionately, while they mentally laughed. These little spats were games for them, a way that they showed they cared. Besides, it was the only way Holly could match wits with her husband. It was nice to know and feel like his equal.

Ritsuko, however, raised an eyebrow in surprise, and turned to Shinji, "Are they always like this?"

"No," he answered truthfully.

The doctor then turned to the other two, "It may be none of my business, but have the two of you ever seen a marriage councilor?"

They broke off the kiss as Artemis replied, "No need. I have enough PhD's to outmatch any of them. Besides, we do this all the time."

Confused, Ritsuko turned back to Shinji, "I thought you said they're not usually like that."

"They're not," Shinji answered. "They're usually worse. Right, Sensei?"

"That depends on your point of view, Shinji," he answered.

The elevator stopped moving, and Ritsuko led them into a dark room. Shinji began putting the skills he had learned over the years to the test, relying on his other senses and logic to tell him where they were. The room was very large, and judging by the way it echoed, there was something else large in it. It was also mostly full of liquid, something thicker than water. He could hear it swirl beneath them as they walked across a grate-like bridge. He could also hear it sloshing against whatever it was the room contained.

Then the lights turned on, and he found himself staring at a large, purple face. Memories that he had reinforced and filed away for later under his Sensei's tutelage about how to deal with such things came to his mind as everything clicked.

"Evangelion Unit 01. This is why he called me back."