Disclaimer: Evangelion is property of Gainax/Studio Khara; If I owned it, I wouldn't be writing fanfiction. I don't own Deus Ex, either.
This is the sequel to 'Make Yourself a Legend'. I highly recommend you finish that story to understand some of the points you'll see here.

EVA: Gods Made From Men

Chapter 1: Lucky Man

Early Summer, 2015. In an apartment belonging to Misato Katsuragi on the shielded dome city of Tokyo-3...

He had white horses and ladies by the score, all dressed in satin and waiting by the door.
Ooh, what a lucky man he was. Ooh, what a lucky man he was...

He had long given up on the waterlogged SDAT tape player he owned of his late father, and was now listening to old rock songs in English on his new Galaxy Gear 3 computer watch. That UN paycheck he received was finally worth it; seeing as how he wasn't fighting for his life anymore, he no longer felt like a piece of disposable equipment. Now, his commanding officer ordered him to pursue a more academic target: Colonel Katsuragi had ordered him to start learning fluent spoken and written English, as Japan's branch of the NERV Special Agency had reached astronomical levels of fame and influence after the dispersal of documentation proving the Japanese Military's betrayal and surprise attack on their former ally, and now the leadership and primary personnel of NERV-Japan were international icons- able to issue demands straight to the United Nations -in addition to the successful defenders of humankind's right to survive. With their new power came a new need to communicate, and as such, he found himself reading, writing, and speaking the UN's version of international English almost exclusively.

His immediate superior, a skilled but unorthodox young English woman, had sugested he use language tools on the Internet to study, and gave him a treasure trove of British culture to immerse himself in: A television series starring a time travelling English Doctor, an English comedy troupe's series' and films; particularly one film mocking and skewering the legend of King Arthur, a series of books and films centred around an English MI6 Agent that reminded him of Colonel Katsuragi's fiancée, the legendary Sherlock Holmes treasury, and albums from famous English musicians. She had given him excellent music, from sources such as the loud and hard Led Zepplin and Eric Clapton, the deeply philosophical Pink Floyd, and the eclectic Emerson, Lake and Palmer; whose lyrics he and his lovely, constant companion were now contemplating.

White lace and feathers, they made up his bed; a gold covered mattress on which he was laid.
Ooh, what a lucky man he was. Ooh, what a lucky man he was...

"Does 'luck' come with the possessions of royalty, Shinji? This song appears to describe a medieval lord or king." She asked from her position, curled up against his side. They were sharing a pair of earbuds and were both exhausted, him from another long day of drills and tests from his war machine, the building-sized Evangelion Unit-01, and her from a day of physical therapy and exercise, and college preparatory studying.

To be fair, their life had been relatively...normal in the months following the Japanese Special Defense Force's failed sneak attack on their lives. First Lieutenant Shinji Ikari, 15 years old, remained one of the two Evangelion Pilots in Japan, tasked with defending the country from extraterrestrial or supernatural threats, neither of which had appeared since the 'death' of the Second Angel, one of a progenitor race of beings that attempted to absorb all life on Earth. His time was spent between staying on reserve alert and learning the UN's administrative language, while -retired- First Lieutenant Rei Ayanami, also (sort of) 15 years old, prepared to enter her first year at Tokyo-3's premier research university; she was genuinely brilliant for her age, evidenced by her acceptance and scholarship. The first day of school was still a month and a half away, but she needed all of that time to recover from the extensive injuries she endured during the campaign against the Angels. Now, she was spending her days either performing physical therapy exercises, swimming (to Shinji's delight and embarrassment, as he still couldn't swim as excellently as she can, but he never argued with watching her glide through the water in a swimsuit), or studying early for her entry into the medical school at Tokyo University. She had spent the entirety of her childhood in hospitals and laboratories, and though she was conditioned never to complain or feel concern for her status, she hated it. Now, with the conclusion of her military career, she'd decided she would put her considerable intellect to work improving children's hospital stays after recieving a pediatric medical doctorate.

"I think it's saying that he's lucky because he's successful, Rei, not the other way around. I know for sure that I never felt lucky until after all the crap we've been through ended..." He shifted on the couch they were cuddling on, awkwardly trying to get more comfortable against the girl molded into his side.

He went to fight wars for his country and his king. Of his honor and his glory, the people would sing.
Ooh, what a lucky man he was. Ooh, what a lucky man he was...

"You know...I'm glad most people don't know it was us in the Evas. I couldn't handle the constant attention. Honor and Glory, nothing."

"Don't you take pride in your accomplishments, Shinji?"

"Sure I do, but I don't brag about them. Now, I might brag about you..." He started tickling her around her waist and navel, hearing the soft laughter that reduced his brain to mush. "I'm happy things are better, Rei."

Her breathing slowed and she melted into his warmth. "I am too, Shinji. I once felt that death, for me, would be relief; your father's plan would offer me the comfort and release from the pain I'd been conditioned to accept. Now that I have so much to live for, I plan leave the world a better place than I entered it."

"You wanted to die that badly, back then?"

"When you know that you were born to be a doomsday weapon, you can have very skewed priorities. But that part of me is gone, now. I can feel my strength returning more and more each day. Waking up to your kiss each morning is what I really look forward to." He humoured her.

A bullet had found him, his blood ran as he cried, no money could save him, so he laid down and he died.
Ooh, what a lucky man he was. Ooh, what a lucky man he was...

"Maybe our story won't have a tragic ending like his did..." Shinji thought out loud as the music ended. He looked down to see that Rei had already fallen asleep. He looked out at the starry sky through their window. = But I should know not to tempt fate like that... =

Inside a darkened room...

SEELE-01 SOUND ONLY: "If Instrumentality is impossible due to the destruction of our target, then the contingency must be enacted."

SEELE-03 SOUND ONLY: "The Singularity, really? That's your solution? It will take decades before the majority of the world's population is integrated."

SEELE-01 SOUND ONLY: "And? Is it not necessary to prepare decades ahead of our goals?"

SEELE-03 SOUND ONLY: "Yes, but neither biointerface has moved beyond the prototype stage-"

SEELE-05 SOUND ONLY: "Incorrect. The mechanical biochip is being readied for distribution by Tai-Yong as we speak. Only the nanite biochip is still on the drawing board."

SEELE-03 SOUND ONLY: "And? The mechanical chips have a 100% rejection rate from living hosts. The volume of Neuropazine the subjects must consume to prevent rejection provokes mental degradation within months; your test subjects are dying from degenerative brain conditions in their twenties! If we allow your 'solution', the entire world will die from Alzheimer's and we'll have nothing to lead! What good is our dominion over the world if there's nobody to serve us? Only the nanite solution is capable of integrating without killing the human being it is modifying."

SEELE-02 SOUND ONLY: "If your tirade is finished, you'll know that Sarif Industries in the United States has working prototypes for both a mechanical and nanite biochip; of course they'll be trying their damndest to prevent that information from slipping. We need to only 'encourage' them to accelerate their production and we'll have the holy grail of technology: Augmented, constantly infolinked human beings that don't suffer the rejection issues or massive disfiguration that mechanical prosthetics bring."

SEELE-05 SOUND ONLY: "Perhaps Tai-Yong should simply acquire Sarif..."

SEELE-02 SOUND ONLY: "Next to impossible; David Sarif is as shrewd and independent as Zhao Yun Ru herself, he won't be overcome unless the other company runs itself out of business in the process."

SEELE-01 SOUND ONLY: "Nevertheless, the information age is our replacement for the biologic rebirth of humanity, and our control of human enhancement is what will allow us to rule the post-human race. That said, our next order of business is to finish the little thorns at NERV. Nagisa, Ikari's bastard offspring and that apparently immortal little girl all need to die."

SEELE-05 SOUND ONLY: "We know that the Third and Fifth travel to and from the GeoFront every day. How humiliating it would be for NERV to watch as its most important assets fall before their very eyes. Let me handle their elimination, it will let me prove the power we really have over them."

A/N: I bet none of you would ever expect somebody to convincingly crossover Deus Ex and Eva, would you? Mwhahahaha