"So this is what the Dirac Sea's like," mused the young lad floating throughout it. How long he had been here he didn't know. All he could remember was that he had usurped the power of Unit-01 from that his mother, the madwoman Yui Ikari. Oh how he detested that woman. All of the pain and suffering he'd been forced to suffer throughout his short life had been set up by her to accomplish her goal of "Immortalizing Humanity."
"Immortalizing Humanity huh," snorted the lad.
The reality was that Yui had simply desired what all mad scientists wished for in some form or another; to surpass the limits of humanity and become its god. She had played everyone one she knew in her quest of insanity. From the emotionally crippled Gendo to SEELE itself, they all had been blind to her ambition and how she manipulated them. She would have succeeded had it not been been for the lad floating in the Dirac Sea, her son Shinji. After initiating Third Impact she came to him out of the Eva, asking him to pass on its power to her to accomplish her goal. She expected Shinji to have been broken down enough to willing do so after explaining her plan. What she didn't expect was for Shinji to throttle her very soul out of existence and taking the Eva's power for himself.
"Bastard! You dare to go against your mother! It was me who saved you when you could not activate Unit-01. It was me who forced it to released you after it absorbed you during your fight with Zurel."
With tears in her hysterical eyes Yui asked, "why do you turn against me Shinji? Everything I've done was to ensure humanity's existence! What has made you opposed this noble goal?"
Shinji had looked her dead in the eye and quietly said, "because mother, humanity did not require its legacy to be preserved. Because the majority of humanity did not ask for their souls to be merged into one mass. You destroyed the planet to acquire the power of a god." He motioned to the Earth, its surface covered in crosses and LCL. "You saw yourself superior to the rest of humanity, never questioning whether or not the rest of us would wish to become one. You forced me to live out the lives of those two billion souls and not a single one wished for this. Simply put, you are nothing more than a demon, an enemy of the humanity you tried to 'save'. To grant you the power of Unit-01 would be the most irresponsible thing I would have ever done. That is why you must die."
With those final words he eliminated her soul, preventing any chance of her reappearing. He went on to absorb Unit-01's power and used it to reform the world, preparing it for the time when humanity found its individuality in the future. Afterwards he opened a portal to the Dirac Sea, having decided that there was no need for him to be around when that time came. Now here he was floating in the Dirac Sea, awaiting to see what world it would lead him to.
"Time for a well-deserved rest," he mused darkly as he closed his eyes. Slowly the images of all he had gone through began to fade away, leaving his mind empty and allowing him to sleep like a babe. The body of Unit-01 continued to careen aimlessly in the Dirac Sea waiting for the time it would be needed.