Got this idea after watching the rather bittersweet good ending of Girlfriend of Steel. Enjoy.
"In that world, all I ever felt was pain. I couldn't stand it anymore."
"Because you couldn't understand the people around you?" – Rei asked from above him, the softness of her bare thighs under his head being the only physical sensation he felt.
"Nobody understood me either."
"Did you try to reach out to them?"
"I wasn't strong enough. I was weak... and dishonest... and only ever hurt people." – Shinji glanced at the cross in his hand. – "Misato, Asuka, Toji, Kaworu... everyone suffered because they were near me."
He neither saw nor felt Rei looking up as she replied. – "But you were able to reach out and connect with another, didn't you?"
What he did feel was the small hand touching his own.
"Shinji..."
He opened his eyes to see another pair looking right back at him. A pair of gray-blue, framed by short hair and a smile.
"I missed you."
Shinji slid his hand over hers and pulled it to his face, inhaling deeply the fragrance that so far only existed in his mind as a memory. Finally, a tear rolled down his cheek. – "Mana..."
A short while later, he felt Rei's soft pressure under him slowly fade and vanish. When he opened his eyes, Mana was lying next to him, eyes locked with his and hand still joined with his.
"Are you real?" – he asked.
"Are you?" – she asked back.
"I want you to be real."
"Same here."
"But you left."
"You never said goodbye, you know."
"Because I didn't want you to leave."
"I didn't want to leave either." – Slowly, her hand shifted and intertwined her fingers with his. – "I never forgot about you. Not once."
"How did you find me?"
"Ayanami-san called me. I don't know how; I just felt called."
"So you came?"
"I wanted to see you again. And... you came to me when I was in the hospital."
"Were you happy that time?"
Mana nodded. – "Are you happy that I'm here now?"
"...I think so."
She gave him a sad smile. – "Do you know what I want now?"
"What?"
"I want to be with you. I don't care what happens to me anymore... but I never want to leave you again." – A tear ran down her cheek. – "I wouldn't be able to bear it a second time. Not again..."
He clasped her hand a bit tighter at that. – "So... you think we should stay here?"
"I don't mind where we are. Whether we're in this world or the real world, it doesn't matter... as long as I can be with you."
Even though months have passed, he still remembered the smell of the lakeshore they visited during their first – and only, before fate forced them apart – date. Mixed with the fragrance of Mana leaning against his shoulder as they sat on the shore, hands joined while watching the sunset just like back then, it reminded him of the happiest time he ever had in his life.
"Shinji-kun?" – he heard her voice.
"What is it?"
"...I'm sorry I hid things from you."
"It's okay."
He felt her shake her head. – "It's not. I know it hurt to find out that I... was a spy. But there's one thing I never lied about."
She snuggled closer to him.
"...I really did like you. And... I still do."
They sat in silence for nearly a minute.
"Are you really okay with me?" – he asked eventually.
Mana's response was accompanied by an almost audible smile. – "I don't want anyone else."
"But... you deserve better."
"You're not as weak as you think." – she replied, caressing the back of his hand with hers. – "You took me from the hospital and helped me escape, even though you knew what would happen if the military caught us."
Shinji felt a small pressure in his hand. When he looked, next to Misato's cross was a small, red pendant he was quite familiar with.
"I couldn't leave you after all that happened." – he murmured, running his thumb over the red gem.
"That's what I'm talking about."
"But what about everyone else?" – Shinji insisted. – "Toji got hurt because I was a coward, Misato-san got hurt because she was protecting me, Asuka got hurt because I couldn't get there sooner-"
He couldn't say any more before Mana laid a silencing finger on his lips. – "Now you're just looking for excuses to blame yourself. Cheer up a little." – When she saw he wasn't going to say anything, she took the finger away. – "You were trusted with everyone's lives. That's a lot of responsibility and I couldn't have done any better than you did. Nobody could have." – She raised her head off his shoulder and softly nudged his jaw to make him look her in the eye. – "But it's over now. You don't have to hurt any more. And... I don't want you to hurt either."
"And if I can't stop hurting?"
"Then I'd rather be hurt instead."
Shinji's head dropped a bit. – "I don't want you to hurt because of me."
"Then let's share it." – she replied, slightly rising to meet him.
"What?"
He could feel her breath on his lips as she whispered – "Everything. The good and the bad."
Their lips touched.
Of course, this wasn't the first time they kissed but Shinji still missed it. Mana was one of only three people Shinji ever kissed and of those three, the only one he ever actively yearned to kiss again. Inside Instrumentality however, even a kiss was more than just simple physical contact: in that instant, their very souls touched and caressed each other.
To love and to be loved. It was like a healing salve to wounds no cure exists for, something both of them understood at that moment.
"So... this is what Ayanami was talking about." – Shinji murmured once the two of them separated. – "To connect with people..."
"Indeed."
Kaworu appeared in front of them.
"To love is to connect above and beyond all boundaries." – the Angel continued. – "If people love each other, they can draw strength from this connection to surpass their own limits."
"That's why you said you loved me?" – Shinji asked.
The Angel nodded. – "I wanted you to persevere and carry on. Angels cannot experience love anywhere near as strong as Lilim do." – He smiled. – "That is what has drawn me to you."
"Love?"
"The love you felt for her. As well as the hope that one day, you'll see her again. That's what kept you going in your heart, even if you haven't realized it. And that's why you resisted Instrumentality: because you would sacrifice your own happiness for her sake, just as you have already done before. It was not instinctual or forced upon you by circumstances. When you were given a choice between humanity and your beloved, you chose her without thinking. To fill the void in your heart caused by her departure, you reached out to her once more."
Shinji heard Mana suppress a sob. When he turned to look, he saw her staring back at him with teary eyes and hand over mouth. – "I... did it really hurt that much?"
Swallowing to briefly clear the tightness in his own throat, Shinji forced out – "More than anything."
She buried her face in his chest. – "Shinji-kun... I'm sorry... I'm so sorry..." – she whispered between sobs. Shinji buried his own face in her hair and cried with her; two souls releasing every tiny scrap of pain and suffering they endured in the past months, holding onto each other in a turbulent world.
"This is the pain both of you had to live together with." – Kaworu spoke eventually. – "Lilim hurt each other even without meaning to. Yet you still reach out to each other, despite that pain. It is this perseverance that makes those connections meaningful."
"Instrumentality makes people able to connect without hurting each other." – Rei added, walking out from behind him. – "To fill the voids in our hearts, it complements us with each other."
Shinji wiped his eyes and swallowed before replying. – "But... it connects us with everyone." – He looked up at them. – "I... I think I understand now."
"What?" – Mana asked.
Shinji looked back at her. – "If we're all connected, what makes us different from each other? If we're always connected, how can we learn how to connect with each other?"
"If everyone is connected with everyone else, what makes those connections different from each other?" – Mana added.
Shinji nodded at that. – "How can we be happy if we don't know how to be sad?"
"How can we love if we don't know how not to love?" – Mana finished his thought.
Kaworu smiled at that while Rei asked – "You reject Instrumentality, then?"
The two looked at her and after a short contemplation, answered simultaneously. – "We don't need it."
The next instant, the world around them shattered like glass.
"Nee..." – Mana murmured as the two of them looked at the apparition of Earth below. They both knew it wasn't quite real but seeing the watery ripple before them, they somehow knew they were at the threshold to the real one.
"Hm?"
"Remember the last day we spent together?"
"Yeah."
She tugged his hand closer. – "After the train left... I cried for hours. I thought I was never going to see you again."
"I didn't." – Shinji said. – "I wanted to cry but the tears didn't come. I wanted to scream but I couldn't." – He looked away, eyes downcast. – "I didn't cry when Ayanami died either."
"But it hurt all the same."
"Of course it did!" – he shot back before reining in his outburst, fully knowing that it was undeserving for Mana. – "She didn't deserve to die... of course it hurt..."
"That's what matters." – Yui Ikari assured, laying a hand on Shinji's shoulder from behind.
The three stayed in silence for a while, broken only by the almost inaudible sound of waves.
"Are you really going to stay in the Eva?" – Shinji asked eventually, the teens turning to face Yui.
Yui nodded. – "I know it was selfish of me to want to do this myself... but forcing someone else to do it in my stead would've been much worse. I understand if you're angry and betrayed; you have every right to feel that way towards both me and Gendo. But even if you do, please don't hate your father. He acted for my sake, even without fully understanding the circumstances. I know he caused you much pain but in his heart, he always hoped that you would forgive him one day. And above all, never forget the greatest gift he ever gave to you: he and I brought you into this world together."
"That's true." – Mana admitted. – "If Shinji-kun weren't born, we wouldn't have met."
"You're more like your father than you think." – Yui added. – "But I know you can stand on your own feet now."
Shinji both felt and saw his mother's presence fade. – "Thank you. For everything."
Yui smiled warmly before looking at Mana. – "Please take care of my son." – With that, she was gone.
Alone once more, the two turned back to each other. – "So I hear you play the cello." – Mana quipped in a casual tone.
"I do."
"When we go back... will you play for me?"
Shinji nodded, a small smile gracing his features. – "I will."
She grinned. – "It's a promise, then. I'll hold you to that."
Reaching into his pocket, Shinji fished out the pendant and held it out to Mana. – "Can I put this on you?"
Her grin softened. – "I gave it for you to keep."
"I know... but..." – He slowly reached around her neck and clasped the chain together before stepping back and smiling at the result. – "I think it looks better on you. And... as long as we're together, does it matter which one of us wears it?"
She cast her eyes down. – "Shinji-kun..."
"Hm?"
"Thank you... for believing in me."
He reached out and joined hands with her once more. – "So... are we going?"
She gave his hand a small squeeze. – "I'll be right behind you."
As consciousness slowly returned to him, Shinji was assaulted by a wave of nausea and weakness. He could barely move and every twitch made him want to puke. The intense stench of LCL didn't help matters either; he never liked that smell, even before learning where it came from.
He still wished he never learned that.
Trying to sit up ended with him falling to the side and getting a face – and mouth – full of sand. Even so, his eyes immediately found her.
At the edge of the water was Mana's still form, the pendant hanging from her neck. As Shinji watched, her hand slightly twitched.
With titanic effort, Shinji dug his hand deep into the sand and dragged himself forward.
First the right.
Then the left.
Then the right again.
Every muscle in his body screamed from agonizing pain but he kept going, the waves lapping the shore, his body dragging itself along the sand and his own ragged breathing being the only sources of sound.
The last of his strength ran out just as his hand fell onto hers.
Even without seeing, he could plainly feel her hand slowly closing around his.
And there you go. For those who haven't seen GoS, I heartily recommend you do so. As rushed as the story felt and as transparent and aggressive her advances were at first, the ending made it clear to me that Mana really did love Shinji – and did so in a way Asuka or Rei never did. On the other side of the coin, Shinji was also attracted to her in a decidedly non-sexual way unlike the dynamic he had with Asuka, Rei and Misato; that is why I think that he most definitely returned her feelings.
Anno revealed in a recent (October 2014) interview that his mental health almost collapsed once more from the strain Rebuild put on him but he stood back up with help from his wife and his best friend Hayao Miyazaki, meaning that he actually took his own message in EoE to heart. This is the ultimate evidence that what we've seen back then wasn't crazy rambling; Anno poured his very heart and soul into Eva and it almost broke him, not once but twice now. I think he more than earned the right to take a break after Rebuild ends, and he stated he's going to do just that. However, he also reiterated his earlier promise from years ago that he's not going to stop the Eva bandwagon after Rebuild. Thus, I sincerely hope Mana will return one day in an animated work.