Shinji gasps for air and, surprisingly, gets it. He opens his eyes and sees a the ceiling of the Eva cage, but something is different. As he looks around he figures it out. 'Who are all these people?' He tries to move but the effort knocks him back into unconsciousness with that thought echoing through his brain. Commander Fuyutski sits, staring at the monitor. 'Who is he, and why does he look so familiar?'. Sub-commander Ikari only has one thought in his mind.
"Retrieve him and have him taken to a holding cell."
"Yes commander." Once the guard is gone, Fuyutski turns to Ikari.
"You have something on your mind. What?"
"That's my son, professor."
"What? How is that possible?"
"I don't know."
"Find out."
"Yes, professor."

Shinji wakes up to darkness. He sits and feels himself to be sure he is still intact. As he tries to remember the events that lead up to this, it hits him like a ton of bricks. He had been absorbed into the Sea of Driac during the last battle, and his battery power had run out. 'If it did, how am I still here?' Then, a clanking can be heard as the door is opened and light pierces the darkness. Shading his eyes and cringing, Shinji hears a familiar voice.
"I will remain with him. Alone."
"Yes sir." Shinji opens his eyes
"Father."
"My son, how is this possible?"
"Why do you care, all you ever cared for was for yourself."
"What do you mean?"
"I thought I was pretty clear."
"Son, I have done nothing but care for you, what Commander Fuyutski did was out of my power, I love you son."
"Commander Fuyutski?"
"Yes, Commander of NERV"
"What's going on here? Where's Misato, I want to talk to Misato!"
"Misato? Oh, Major Katsuragi. How do you know her, and why would you want to speak with her?"
"Stop whatever games you're playing and let me see Misato!"
"Calm down son. Please, calm down"
"I WANT MISATO!"
"YOU WILL STOP THIS INSTANT!" There was a hard gleam in Gendo's eyes, and steel in his voice. Shinji falls silent.
'What is he up to? Why would he do this?'
'How can he be here? How, how, HOW?'

As Gendo's echo dies, the sound of approaching footsteps can be heard. The door opens, and in steps Yui Ikari. Her eyes fall straight to Gendo and she steps next to him, looking him in the eyes.
"I came as soon as I heard, is it true?"
"I'm not sure. He looks like our son. Maybe it is true."
"How could it be?"
"I don't know."
During this, Shinji's eyes have gone wide, and his mouth moves, but no words come out. Finally, he is able to rasp out one word.
"Mom." Yui turns sharply and sees Shinji. Her eyes go wide and she takes a step backward, into Gendo's arms. There is her son, alive and well. Her eyes well up with tears.
"Shinji!" She breaks free of Gendo's arms and hugs Shinji. They are both crying.
"Yui, are you sure this is Shinji?"
"Yes. I don't know how he's here, but it's him. It's our Shinji!" Gendo takes a step forward, helps them both up and embraces them.
"You're alive, I don't understand how, and I don't care, you're alive!"
Shinji attempts to speak through the sobs, but is unable.
"It's ok, it's ok, mama's here for you, mama's here. Just let it all out."
"Mom... how?"
"What?"
"You.... you're dead. I've seen you. Inside my Eva. How?"
"He's in shock, he's hallucinating. Let's get him out of here and into the hospital."
"Yui, I don't know..." "DAMNIT Gendo, this is OUR SON."
"You're right, we'll get him out of here, somewhere comfortable." Gendo goes to speak with the guard.
"Shhhh it's alright baby, it's alright. Mama's here. Mama's here."

Shinji returns to consciousness peacefully to find Yui sitting by his bed. He stares at her, without making any noise, just staring at her in utter disbelief.
'How.' The question echoes through his mind as he slips back into unconsciousness.
Yui looks over at her peacefully sleeping son. Everyone always said how much he looked like her, but she had always seen more of Gendo than herself in him. He had the same deep blue eyes that had made her fall so deeply in love, the same jet black hair. She leaned over, kissed his brow, and wondered to herself what she had done to deserve such a miracle.