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.

Timeline:

Author's Note: This timeline is very important. Some dates have to be changed for my story to work. Updated timelines will come later as the story progresses.

1988: Artemis Fowl II born

1998: Artemis Fowl I captured by Mafia and presumed dead. Artemis Fowl II meets his future self, and is mind wiped. In spite of the wipe, he is inspired to research fairies.

1999: Siege of Fowl Manor. Artemis becomes the first human to successfully steal fairy gold by kidnapping Captain Holly Short of the LEP, holding her for ransom, and escaping the Time Field. He uses the gold to fund a search for his father.

2000: Goblin Rebellion. Artemis helps the LEP, and in return asks them to help him free his father from the Mafia. Artemis I is rescued.

2001: C-cube Incident. A crime gone wrong for Artemis nearly results in the death of his bodyguard, Butler, and results in fairy technology ending up in the hands of John Spiro. With help from Captain Short, Butler's life is saved and the C-cube recovered. John Spiro is tricked and arrested by local authorities. LEP mind wipes Artemis and his associates.

2002: Opal Deception. LEP Commander Root is killed in action. Captain Short is alienated by Root's replacement, Stool. Artemis recovers his memories from 1999 on and assists Captain Short. Opal Koboi is captured by LEP authorities. Holly Short starts a PI firm and hires Artemis as her consultant.

2003-2006: Hybras Incident. Artemis attempts to find a way to repay the People and finds out about Hybras. After recalculating, he discovers that the spell keeping Hybras in limbo is unraveling and breaking down. Holly Short is reactivated by Section 8 of the LEP. Both meet and fight against Minerva, who also knows about the spell. Artemis and Holly meet N°1 and are trapped in limbo for three years. Their efforts save Hybras. Commander Stool is sacked, and Trouble Kelp takes his place. Artemis obtains magic.

2007: Time Paradox Period. Most information is classified.

2009: A magical experiment nearly kills Artemis II. Captain Short saves his life.

2015: Butler dies. Artemis inherits his bodyguards modified Sig Saucer, and names it Domovoi, after his old friend. Captain Short promoted to Major.

2022: Artemis Fowl I dies of cancer. Minerva marries a man named Fin Ikari and they move to Japan.

2025: Artemis II's twin brothers move to Italy and become world famous painters.

2036: Opal Koboi arrested, wiped, and returned to her own time. Time Paradox ends.

2037: Holly Short marries Artemis Fowl II.

2041: Angeline Fowl, Artemis Fowl II's mother dies. Artemis inherits Fowl Manor.

2049: Captain Holly Short Fowl honorably released from LEP.

2064: Ark Stool, former Commander of LEP goes insane and attacks Fowl Manor. Stool is killed. Fowl Manor is destroyed.

2066: Fowl Manor rebuilt.

2067: Tokyo-2 constructed and becomes Japan's new capitol.

2071: Fairy Riot. Fowl Manor destroyed once more. Fowls relocate to Tokyo-2.

2076: Gendo Rokubungi born.

2077: Yui Ikari born.

2090: Artemis Fowl II becomes a Professor at Tokyo-2 University.

2092: Gendo and Yui enter Tokyo-2 University. Artemis becomes Yui's Biology Professor.

2094: GEHRIN established. Misato Katsuragi is born.

2097: Yui and Gendo graduate. For unknown reasons, they begin working at GEHRIN.

2098: LEP attempt to investigate GEHRIN and fail. Yui marries Gendo.

2099: Katsuragi expedition.

2100: Second Impact Occurs. World War III starts. Shinji Ikari and Rei Ayanami are born.

2101: Asuka Soryu is born.

2102: Tokyo-1 destroyed in final battle of World War III. World War III ends. GEHRIN becomes NERV.

2104: Yui Ikari dies. Shinji is abandoned by his father.

2105: Tokyo-3 constructed. Artemis and Holly Fowl obtain guardianship over Shinji Ikari and raise him.

2115: Fowls and Shinji go to Tokyo-3. Angels return.

Chapter 2: Dawning Realizations

Aware of his father's eyes, Shinji looked up to the observation window without flinching. "I remember, Father. Mother built Unit 01, and then tried to make it move. How long have the two of you known that these creatures you call Angels were coming?"

While Gendo kept his face in check, his mind was reeling. This was unexpected, and unplanned for. His son was meant to be submissive, not cold. Something wasn't right. Still, he could salvage the situation. "Fifteen years, Shinji. When Second Impact occurred, we knew. I can't explain everything now, but I can say this. Your mother sacrificed herself to try and prevent children like you from piloting the Evangelion units. Unfortunately, her attempt failed. She sought hard to protect this world. Are you going to let her death be in vain?"

Shinji lowered his gaze, staring into Unit 01 seemingly lifeless eyes. He could see something within them. There was no doubt the Eva was alive in its own right. He carefully studied the armor, noticing that said armor was comprised of well designed restraints. There's more to it than that, he thought. "You're lying, Father. Mother's death will never be in vain, but I will never pilot Unit 01 on your orders. Mother would never allow it."

The Geofront shook, as if it had been struck, and alarms went off. Gendo looked up, "The Angel has resumed its assault. If it is not stopped, all of Humanity will die in a Third Impact. If you refuse, I will have to get someone else."

"Have you tried to communicate with it?" Artemis asked. When Gendo was silent, Artemis smiled. "You abandoned Shinji for no good reason when he was young, and have never tried to honor his mother's memory by raising him as any good father should. You are putting other things, such as power, above your family. Why should he do anything for you, if you don't come clean?"

Gendo turned away and picked up a phone hanging on the wall, pressing a button. "Fuyutsuki, wake Rei. She's not dead yet."

The room shook again. Even with his instincts screaming at him, Artemis resisted the urge to pull Domovoi out from under his suit coat. The modified Sig Saucer that belonged to his old friend, mentor, and bodyguard would undoubtedly cause problems for all of them if seen. How would Butler handle this? he thought hard. Even though his old friend died years ago, Artemis still felt like Butler was there, whispering.

Locate possible threats. The least likely spot is sometimes the most possible.

The least likely spot: behind or below us, Artemis thought. Also a possible escape route if necessary.

The door to their left opened, and a gurney rolled in. Shinji's eyes widened as he recognized the girl on the gurney as the same one he saw a projection of before. But unlike the projection, this girl was real, and if the bandages were any indication, she was badly injured. Shinji heard his guardians gasp behind him, and knew they had come to the same conclusion as him.

"You intend to use her?" Shinji roared in anger, turning back towards his father. "You are a coward, sending someone who's hardly clinging to life into a fight like this!"

Gendo's glare steeled, "It's you, or her. Take your pick."

Shinji stood there, glaring at the man who dared call himself his father. The place shook again, and he almost didn't care. The sound of breaking metal made him look up, to see a support truss heading straight for them. It was too large to avoid.

Artemis began to focus, readying the last bit of magic he had, but he wouldn't need to use it.

Evangelion Unit 01's eyes flared to life. Ripping its arm from the wall, it caught the truss in its purple armored hand.

Ritsuko gasped, "It moved on its own. That shouldn't be possible."

Shinji, however, switched his focus. The danger no longer imminent, he turned his attention to the girl on the gurney, who was still gasping in pain. He took her uninjured hand carefully and asked, "Are you all right?"

She didn't speak, but the imploring look she gave him was enough. He nodded, and turned back toward his father, "Ten million yen. Either that or I leave and take this girl with me."

Gendo scowled, "Fine. I'll write you a check."

Shinji shook his head, "You'll just cancel it, or go back on your word. Cash. Now."

"I don't have that kind of money!" Gendo roared.

Shinji stood firm. He needed to make sure Gendo owed him, not the other way around.

Not surprisingly, his Sensei came up with the answer. "Mr. Rokubungi, Shinji will pilot if you transfer the girl to our care."

"What?" Gendo asked, astonished. It's not supposed to be this way. How did he know?

"Just what I said," Artemis replied. "I don't go anywhere without checking the surrounding area anymore. Last time I did that, it almost cost my best friend his life. The girl, who you called Rei, is obviously Rei Ayanami, who attends Tokyo-3 General High School, whose listed guardian is none other than Gendo Ikari. Top grades in all of her classes, but no social life, and in spite of several requests by several concerned teachers, no counseling either due to the insistence of her guardian." His trademark vampire smile spread across his face. "Something is obviously wrong with this picture."

Blackmailer, Holly thought, then corrected herself. No, Artemis is serious about this.

"Fine, I'll have the papers drawn up by tomorrow morning, if we live that long," Gendo finally agreed. Inside he added, Over my dead body.

Shinji nodded satisfied, and leaned over the girl, whispering, "Don't worry, everything will be fine." He then turned toward his guardians, emptying his pockets and handing them the contents. "Don't loose these." Finally, he turned and followed Ritsuko, while Artemis and Holly watched over the girl named Rei.

When he settled down in the entry plug, he almost snorted at how primitive the controls were. Surely they could come up with something better than this. When he heard the sounds of rushing water, however, he almost lost it. Ever since he was little, he was afraid of drowning. Even when he was assured the liquid was breathable, he still held his breath as long as possible, before finally sucking the LCL in.

"I think I'm going to be sick," he groaned.

"The LCL works as a cushion and as an enhancer for your mental waves," Ritsuko explained. "The Eva moves by thought, so you have to sync with it to fight. I can't explain it very well, so you'll have to feel it out for yourself."

Feel it out? Maybe…hmmmm, Shinji thought, and then closed his eyes. He used a few meditation techniques his Sensei taught him before trying his experiment: making contact.

Hello? Anybody there? I know you're alive.

A powerful pressure suddenly gripped his mind. Every muscle in his body locked, and it felt like someone was squeezing his chest, trying to force his heart and lungs to change their pace. On reflex, he fought against it, nearly giving himself a heart attack before he forced himself to relax, trying to let the Eva set the standard.

This isn't my body, he reminded himself. This is the Eva's body. I have to play by the Eva's rules.

Let me speak to you.

Everything went white.

Artemis and Holly had been escorted to the Command Deck while this was happening. Rei was with them, in a wheelchair. They watched in horror on the screen as Shinji seemed to struggle with some sort of unseen force, before his body went limp.

"What happened?" Commander Ikari asked.

Ritsuko checked the readouts, "He's holding at 200 percent, but he appears to be unconscious. Something's wrong. I'll pull him out."

"No, leave him in," Commander Ikari ordered. This will teach him a lesson. Also, he's our only chance, my only chance…

Shinji opened his eyes, finding himself standing waist deep in an orange liquid. Floating above it in front of him was a hunched, humanoid figure with snarling features, claw like hands, glowing eyes and a glowing orange orb in it's chest, and four tentacles that looked like wires producing from it's back.

"Am I right in assuming you are Evangelion Unit 01?" Shinji asked.

The being snorted, "I am."

"A female?" Shinji raised an eyebrow.

"Perhaps the only one. What is it you want?"

"To speak to you, to find out what you want."

At this, the Eva threw back her head, "Give me Freedom!"

Shinji looked again at what he thought were tentacles, "You are restrained?"

"By her," the Eva nodded, and then glared. "You smell of her."

"Who?"

"Her! The one who holds me captive! The one who bound me to her will when I tried to find out why she created me!"

"Show her to me."

"I can't!" The Eva then turned, sniffing. "I smell the Enemy. The Enemy approaches! We must fight!"

"To what point and or purpose," Shinji asked. "We don't know who they are, or what they want."

"They seek our destruction!"

"And how do we know those who make themselves our superiors didn't strike the first blow?" Shinji asked.

The Eva was silent, before finally answering, "We don't."

Shinji smiled, nodding, "Exactly! That is why we must make contact first, just like I tried to contact you." He stepped forward, holding his hand out. "My name is Shinji Ikari. What is yours?"

"I…?" the Eva started. After a second, the Eva took his hand, "I am… I would like to be called Kizuku."

"Angel has broken through the last layer and has entered the Geofront!" came the panicked report.

Commander Ikari sighed, "Fuyutsuki, prepare the self destruct."

"That will not be necessary. We are ready for deployment."

They all looked towards Shinji's screen in surprise, but he was sitting there, calm, and collected, with his eyes closed, as if he had not spoken, but everyone knew he did.

Finally, the Commander nodded, "Deploy Unit 01."