Shinji remember when he first came to NERV, hopping to finally get some love from his father when, in fact, he had just been called to become a child-soldier piloting EVA-01 which, at the time, he believed to be a mechanical dragon, in the hope to protect humanity from actual dragons. How he had refused to go inside the Evangelion, until his father called a hurt girl named Rei to take his place. She was a strange girl, with her pale skin, light-blue hairs and red eyes, who he somehow immediately felt a connection with. She was covered in bandage and couldn't even walk, there was no way he would let her pilot! But after what he discovered today, maybe he should have…

Dragons are the only thing Shinji hate more than piloting an Eva. He hated how Evas looked and moved like a dragon, he hated them even more since that time part of the armor broke, learning they were mostly made of cloned dragon flesh, with technology preventing them from moving without a pilot embedded in their body, and with strong armor piece where they should have grown skin. But at least Evas were dragons you could control, not like the dragons who killed his mother.

He still remembered that day. His parents had the good idea to take him to their lab, where they were studying a gigantic but seemingly dead creature, something that, for the longest time, was deemed fictional: A dragon. One of the technicians took a sample bigger than needed and, somehow, made it fall. Young Shinji, who had briefly escaped his parents' vigilance to take a closer look at the dragon, felt something fall on his head and start to move. He ran panicked to his mom, who saw the big morsel of dragon meat on her son head. A dragon sample that was starting to move and transform.

Fearful of what it might be doing to her son, she took it, wanted to trow it as far away as the could. But that little meaty bite had already synchronized with her son, to use the term NERV would later give to the phenomenon, turning into a new dragon who, trying to defend itself from a perceived menace, flung its tail at Yui, sending said mother in the direction to the bigger dragon.

Bigger dragon who, having felt a (former) piece of itself synchronize with someone, was furious. "How dare those inferior beings desecrate my holly flesh? I won't let that go unpunished! I'll absorb all of them! Make them merge with me, body and mind!" it angrily thought. But it was only able to absorb a few peoples before being skewed by the long red spear it had been found, among which was Shinji's mother.

The sample-turned-dragon was a baby Rei in her true form.

For years afterwards, he sometime experienced feelings he could tel weren't his own, but couldn't tell they were Rei's, not knowing of her and the link they have.

"Again with her feeling. Like she has any right to be sad and… Resigned?!" That acted as an electroshock to Shinji. "I'm a jerk…" He lament, running as fast as he cam toward the nearest entrance to NERV HQ. "Here she goes telling me the truth, feeling all guilty about it, and I trow back at her! And now? Now she's about to do something stupid! I can feel it!"

Arriving near the place Rei is, he was accosted by a member of NERV's staff "Ah pilot Ika…" But Shinji don't let him finish, seeing Rei in her true form beyond the door. He had never seen it before, but he didn't know of much dragons with light-blue scales and red eyes. That, and the link between them tell him it is her, anyway. Her four legs were chained and some machinery was all around her. "REI!" he scream as he run toward her. Shinji pull a lever, liberating Rei's legs, before going to the nearest one. Touching it and concentrating, trying to make his friend take her human-like form. It work, but only because she wasn't expecting it.

He get a nude Rei in front of him, but right now he don't care about her state of undress. He take her in a tight hug and cry, repeating "Sorry" on loop.

The dragoness was surprised by the feeling she got from him through the link. Joy, shame and… Relief?! Rei don't understand what's happening. After telling him the truth, he had felt nothing but hatred, fear and distrust toward her. So she had asked the NERV scientist to turn her into a Evangelion. She wouldn't have been able to take on a human form anymore, or even have control of her body, but she wouldn't have a mind left either. That way Shinji wouldn't even need to trust her anymore. But he prevented the procedure? Was happy he was fast enough to do so?

She don't understand, but she is grateful. All she can do for now is take this person she couldn't hate even if she wanted, and patiently wait for him to calm down.

Meanwhile, Commender Ikari Gendo is scowling. The timely intervention from his son might complicate his plans to reunite with Yui. He might need to have First Child kidnapped from under the nose of the Third and turn her into an Eva against her will.

After Gendo's insane plan to exterminate humanity in the vain hope to reunite with his wife was revealed to the world, all former member of NERV were forced to go into hiding, even the unaware participant, like Rei and Shinji.

They were living in a small rundown apartment, Rei wearing a long black wing and contact-lenses to hide her identity. They belived they had been discrete, but apparently they weren't discrete enough since right now they find themselves at gun point the instant they open their home's door. The two lover put their hands above their head, trying to resist would only complicate things.

Rei and Shinji had expected to be either sent to prison or executed. Instead, they are now facing Shinji former guardian and their former superior, Katsuragi Misato, now commander of an anti-NERV organization named WILLE, telling them they are now members of it, willing or not.

The but of said organization? Hunt Gendo and his few remaining allies, SEELE include, while also fighting any new dragon sent by the escaped Adam trying to bring humanity's end.

While still pissed at being forced to join, Shinji is quite impressed by what he is in WILLE HQ. Dragons helping humans survive without needing to be turned into Evas, equipped with some sort of backpack so they can transport troops, said backpack able to turn into clothes when the dragon took on its human form. But since all dragons present have the ability to look human, that mean they all had synchronized with a human, and the dragons weren't that numerous…

The only drawback was that, since a dragon can't speak when in its native form, WILLE had needed to develop implants that let said dragon interface with the comm' system in the backpack. (Which only work in dragon form.) Because of the nature of the implants, needing to be placed in the brain, the operation wasn't without risk, and needed to be done while the dragon was awake. Because of the link, Shinji vividly feel Rei's pain, even from the other side of HQ.

Shinji is devastated. Adam sent a gigantic and powerful dragon to kidnap Rei, and nobody at WILLE had been able to stop him. Worst, he can feel her fighting against Adam's tentative absorb her. He know the other are already there, trying to fight the first dragon, to find a way to rescue the dragoness that had stolen his heart. But being left at HQ, unable to fight, it is very hard on him.

Suddenly he cense Rei escaping. It feel almost like he wasn't able to breath until now, like he's taking his first breath in a long time.

Rei is sure that, with her spectacular escape, the rest of WILLE is trying to contact her, wanting to know what happened. Alas, while she had been able to keep her mind separate from Adam's, at some point her body had been entirely absorbed. Not for long, but it was enough to loose the implants, which were now somewhere in Adam. That, and staying a separate mind doesn't mean not being connected. She now knew more about her own species. Like the fact they had been created by god-like beings calling themselves the First Ancestral Race, to eliminate any intelligent, tool using species, preventing said species from ever evolving into the same god-like state. And they wouldn't like Adam failure to eliminate humanity, let alone the fact she existed.

She also learned that, unlike Adam, all dragons he created were sterile. But her, because of her slightly different birth, wasn't. Oh, she was far too young for that yet, especially since dragons live for millennia, but someday she will be able to give birth to other dragons, without needing help from anyone else, just like Adam. And it terrify her. What if it that future, where Shinji's short life long since ended, she change so much she accept the mission given by the FAR and sentient beings like Adam wanted to snuff out humanity?

A little voice in the back of her head say she won't, that it wouldn't let her do. That voice was the reason why Adam, once awake, couldn't simply birth an overwhelming quantity of dragons and be done with humanity. It was also one of the reason he couldn't merge Rei back into himself, along with her own determination to stay separate and her link to Shinji. It was the voice of someone that had been part of Adam for almost two decades. It was a Dr. Ikari Yui, the long lost mother of her beloved Shinji. That's not something she should hide from him, but… How can she say to her lover that his mother would live in her head from now on without sounding like she lost her mind, nor rethink their relationship?

All Rei know was that, apparently, her new quandary is greatly amusing her mother-in-law.