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Yui Ikari had seen naked men in her office before. Naked, blue men, not as much. Her door was also still locked, so she paid a greater amount of attention to her visitor than she might have otherwise done.
"Hello, Yui Ikari," the blue man said, his Japanese unaccented despite the improbability of his having been raised with the language. "I am Doctor Manhattan. I am here to prevent a disaster. Will you assist me?"
"What kind of disaster?" Yui asked.
The blue man was silent for a moment before continuing. "I am also speaking to a part of you in many future timelines, also attempting to prevent a different disaster. We have finally arrived where everyone is asking the same question, and therefore I can answer all of you at once. You are aware of the situation in the United States in the twentieth century, where the world narrowly avoided a full nuclear war by uniting against a supposedly extraterrestrial threat that caused widespread death in New York?"
"No," Yui said, shaking her head. "That would be very old history to me."
The blue man nodded and waited an uncanny beat before continuing. "The aversion of nuclear war was the brainchild of a man named Adrian Veidt. He foresaw the destruction of Earth and acted to prevent it by introducing a problem that was sufficiently outside the context of the political situation that all nation-states would feel threatened and would unify against the outsiders." The blue man stopped where another man would have drawn a breath, but he did not do so.
"Adrian Veidt's plan succeeded, but even a genius such as he could not foresee the ramifications of his plot. The being that he had brought into New York and destroyed sent a message into the universe, and the universe, recognizing the threat, responded. Earth already has the seeds of its own destruction sown by what you refer to as the First Impact, but those seeds were germinated in response to Veidt's assault. Once a Second Impact revealed that Veidt's attack had not been a historical fluke or a one-time event, humans united against an outside threat, but this one was far beyond its capabilities to control or destroy. NERV, SEELE, all such organizations were doomed to die from the inside, the secrecy, and the complete unwillingness of humans to act with a single mind and purpose. Gendo Ikari understood this, and attempted to merge all of humanity into a single entity, so that they would have the unity they so long craved, but he, too, failed, and his failure dooms humanity to nonexistence in all the timelines that I can see, despite the efforts of the humans that remain to continue."
"Why are you talking to me, then, instead of trying to convince Gendo? He's stubborn, but he can see reason. He would abandon a plot if he had foreknowledge of its failure." Yui frowned. There were ample reasons to believe that this blue man, Doctor Manhattan, was a dream, or perhaps trying to sleep off another one of Misato's party nights, but something about the way he spoke, as if he were certain, rather than speculating, made her want to believe him more.
"You are more important to the avoidance of destruction and the Third Impact than the one who created you," Doctor Manhattan said. "If the body and essence of Yui Ikari are separated, then destruction is assured. The essence will destroy, and the body will be destroyed and recreated repeatedly. You are not doomed, but you must retain your essence long enough to prevent the awakening of absolute terror."
"The AT field is already a known element of Angel attacks," Yui said. "If we were supposed to stop the awakening of the Angels, then we have already failed and the world is doomed."
"Do not allow yourself to be separated," Doctor Manhattan intoned. "Your choices must be in favor of keeping yourself together." Then, in a flash of white, the blue man was gone.
Yui blinked and shook her head. If this was the hangover from one of Misato's bartending nights, Yui was going to inspect Misato's beer and make sure that she wasn't slipping absinthe or something stronger into her drinks.
"What could he have meant by that warning?" she mused. Shaking her head, she pulled up another report on the progress of the Eva Project. Unit 01 was still not doing anything of interest from the tests. If it didn't start showing signs of life, she might have to go inspect it personally.