Title: Messing With The Scenario

Author: Knife Hand

Feedback: Constructive feedback appreciated, flames unappreciated

Spoilers: All of Neon Genesis Evangelion (just covering my basses)

Rating: PG-13

Disclaimer: Do not own Eva. I would buy it but I am broke.

Summary: AU. One interpretation of the series where Shinji has a backbone. Set in 2017, because the Angel attacks are delayed for two years.

AN: Major deviation from Eva Cannon. Timeline elements ignored. Characters are OOC for the series. If you don't like this then stop reading now. You have been warned.

AN2: In this Rei is not a Clone and she is not related to Shinji in any way.

" " denotes speech

' ' denotes thought


Shinji Ikari wandered through the barracks of the UNSF Junior Military Academy, watching his friends and comrades. When his father had abandoned him to his uncle, his uncle had decided that he did not want Shinji either, so he enrolled him in the Academy. That had been when he was five, and now at sixteen, he was lean, fit and hard, moving with confidence and grace. Around him were his classmates, those boys and girls, now young men and women, who had arrived here at the same time as Shinji and had trained with him. Shinji was dressed in a simple green jumpsuit, while his friends were in various states of dress, from their birthday suits to full dress uniform. It was Sunday and as a result, most of the class had free time and were relaxing, dressed similarly to Shinji.

As Shinji wandered, his own little ritual to think and relax, a younger girl, around the age of nine, came racing up to him. He recognised that she was currently assigned to the Postmasters office.

"Letter for you, Sir." She said smartly, snapping off a salute.

"Thank you. Carry on." Shinji said as he took the letter and the girl ran off about her duties.

Shinji took a look at the letter and sighed.

"What's the matter Shinji? Another planning "exercise" for the generals?" someone nearby asked.

"No, Michelle. Temporary transfer orders." Shinji replied.

"Where are we going, sir?" Michelle asked, her bearing changing from a sixteen year old girl to a battle hardened warrior.

"Nowhere, Corporal. WE are going nowhere." Shinji replied, returning to his room to pack.

"Need a hand, Colonel?" came a German accented voice from the door.

"No thanks, Major." Shinji replied to Major Hans Soyru.

"So, Shinji, where you going?" Hans asked.

"Detached assignment to NERV." Shinji replied.

Hans slowly nodded his head, his cousin was involved with them.

"You know any time you need us, the Regiment will be there." Hans said.

"I know, Hans. Unfortunately I don't think that the Regiment will be of help. This is not open combat." Shinji said.

"You know you can take an aide?" Hans said.

"I know. If she'll go, I'm taking Lieutenant Elizabeth Waters." Shinji said.

"Liz? Good choice." Hans said. "I'll go talk to her."

Hans turned to retrieve Liz, when he was stoped by Shinji's voice.

"Who's you cousin, in case I run into them?"

"Her name is Asuka. She's our age, she got chosen by NERV about the same time as I came here. I haven't seen her since."

With that Hans left and Shinji got back to packing.


Shinji walked off the platform towards the rendezvous point specified in his orders. Lieutenant Waters walked crisply beside Shinji, long dark blond hair, kept in a ponytail, fell down her back and her skin was fair but suntanned, while her chocolate brown eyes surveyed the area. Both Shinji and Liz were dressed in full dress uniforms, with their sidearms evident and duffle bags thrown over their shoulders, left for Shinji and right for Liz, so as not to impede their shooting arms. The pair reached the rendezvous point and they were startled by a blue sports car coming screeching up and parking right in front of them. Instinctively they had put their hands on their pistols when the screech had started, and they now removed them as the door opened.

"Shinji Ikari? Name's Misato Katsuragi. Who's the girl?" the purple haired woman in the car asked.

"That's Colonel Shinji Ikari, Captain. And the 'Girl' is my personal aide, Lieutenant Elizabeth Waters." Shinji snapped in a commanding voice.

"Yes, sir. Sorry, sir." Misato replied.

Shinji and Liz got quickly into the car and Misato drove off at a slightly more sedate speed than she had arrived. The long ride from Tokyo 2 to NERV was done in silence except for a call at the beginning where Misato called to check on Liz's security status, which was cleared with an identification code phrase from Shinji. The car parked in the car-train port and the train began its way down. They broke into the Geofront, the funnelled and reflected sunlight shining from vents in the ceiling, nestled among clusters of gigantic floodlights, shining down on a pyramid shaped building amid lush gardens and parks, with a large, man-made lake as a centrepiece.

"Impressive." Shinji said.

As they disembarked from the train, the car being parked by an attendant, the group was met by an escort of section two agents.

"The Commander wants to see Ikari." One of the suited men said.

Shinji, with Liz falling in just behind him, was escorted to the Commander's office.

"Wait here, Lieutenant." Shinji ordered, before entering to see the Commander.

Shinji entered the Commander's office, a cavernous office with a massive desk at the far end. Shinji crossed the floor and stood at attention in front of the desk.

"Colonel Shinji Ikari reporting for temporary detached assignment with NERV." Shinji said formally.

"It's been a while." Commander Ikari said from behind his desk.

Shinji stood silently at attention, ignoring the biting comment from his father.

"Well, interesting. We'll have to take care of the girl, but." Gendo Ikari began.

The Commander was silenced by a Desert Eagle .44 pistol being pointed at his temple, Shinji have jumped over the desk while he had been talking.

"If you ever threaten anyone under my command again, I will kill you. The Lieutenant is here as my personal aide and thus has total security clearance and is under protection by the UN charter that created NERV. Touch her and NERV can be dissolved." Shinji threatened. "Do you understand."

Gendo nodded.

"Very well." Shinji said, skirting the desk and returning his pistol to its holster. "What is my assignment here?"

Commander Ikari outlined the Evangelions, the Angels and how Shinji was able to pilot an Eva.

"Understood. Whenever I am inside an Eva, Lieutenant Waters will be on hand. She will have specific orders to terminate any internal threats to either my or any other pilots safety." Shinji commented, before turning to leave. "It had been an experience, father."

Shinji closed the door behind him, and Gendo let out a sigh. This was not the first time someone had threatened his life, however Shinji was the first who was capable of achieving it.

"This will certainly interfere with SELEE's scenario." Gendo said with a smirk.


Kensuke sat at his desk trying to hack into the school database to find out about the new students. He had already cracked the database, the problem was that these files had extra protection. Kensuke Aida was the schools resident Hacker and military nut, he had been since he was twelve. He cracked his neck and tried to push up the glasses that he no longer needed, having gotten laser eye surgery at fifteen. The door opened and the new students came in. The boy was slightly taller then Kensuke, with brown hair and blue eyes. His bearing exuded confidence and he somehow made the black slacks and white shit of the school uniform seem to be more. The girl had dark blond hair in a ponytail. Her Caucasian complexion was slightly concealed by an even tan and her eyes were chocolate brown. She moved with a fluid grace that made her exotic but she was controlled, in both composure and movement, however she seemed slightly uncomfortable in the dress of the female school uniform. The pair were talking quietly in English, the girl having an accent that he could not quite place. The rest of the class came in by ones and twos, until the Sensei arrived. Hikari, the class representative, stood to do her "Stand, bow, sit" routine, but she was interrupted.

"Atten-hut." The boy called.

The new students, and surprisingly, Rei Ayanami, the blue haired girl who never talked to anyone, all snapped to rigid attention, surprising the entire class.

"At ease." The new boy directed to the new girl, before turning to Rei. "As you were."

Rei then sat down. The two new students now stood with their feet shoulder width apart and their hands behind their backs.

"Perhaps you would like to introduce yourselves." The Sensei said.

"My name is Shinji Ikari." The boy said simply.

"Liz Waters. I'm an Australian Ex-pat." the girl said, explaining her accent.

They both sat down and the Sensei began his lesion, telling about his experiences during the Second Impact, the same topic he had been preaching for the last four years. Kensuke had a distinct impression that they had something to do with the military and he wanted to find out, even if it was only that they went to one of those military schools. With a smile, he began typing, searching for information.