Tony Stark was of course rather surprised when Spider-Man brought a woman who thought she was a ship to him at Avengers Tower... Even more surprised that she was right.
Tony: "... I'm going to need to do a full examination-"
Pepper: "No."
Tony: "Pepper, she is literally a-"
Pepper: "No."
Tony: "Fine. I'll call Richards."
And so, Reed Richards came over to do the examination, humming thoughtfully as he poked and prodded the patient Enterprise in the medical lab. Ben Grimm had come too, but mainly to observe. Ben Grimm of course took this as just another odd thing to happen. Ship Girls...yeah sure...fine.
Reed: "Fascinating! You appeared in River Vale, New Jersey, did you not?"
Enterprise: "Well yes, but how did you-?"
Reed: "That is where the stern plate of the Enterprise is. Probably one of the largest pieces of her still around."
Enterprise: "Ahem."
Reed: "Or should I say, was. The rest of the construct of the Enterprise you carry around is composed of the standard metallic alloys of a military ship constructed during the 1930s and active quantum energy fields. Your body is composed of organic materials but is also held together by these same energy fields, giving off a unique form of radiation."
Peter: "Which means if there are other shipgirls around, we can track them!"
Tony: "Already on it."
His armor was already analyzing the sensor data and he was soon lost in the numbers. Peter walked up to Enterprise with a compassionate expression.
Peter: To Enterprise "What do you remember after waking up in River Vale?"
Enterprise: "Well... My radio picked up emergency calls about a monster in New York. So I rushed down the Hudson as fast as I could."
Peter: "Any other details? Strange people around?"
Enterprise: Frowns "... I do recall seeing someone nearby. A man, I think. He was running away into the street. That's when I heard distress calls."
Peter: "He's probably long gone by now, but it does at least give us a place to start."
Ben: "Was he dressed like a Beekeeper?"
Enterprise: "Not that I can recall."
Peter: "So either not an AIM agent, or an AIM agent smart enough not to wear the suit in public."
Ben: "So... Not an AIM agent."
Peter: "Exactly." Back to Enterprise "So... I mean, do you remember your life as a ship?"
Enterprise: "I do, actually! I remember being constructed, my first sea trials... The war... Losing my sisters..." She looked sad. "Though I've only become a human now, it feels like... Like I felt sorrow at their losses, even before this happened."
Peter: "I'm sorry..."
Reed: "Hmmm! Also fascinating! I wonder if it's retroactive human context applying, or if there was some innate psychic imprinting on you by your crew?" He ran a scanner over Enterprise's head, which she glared at. "Can you share anything else about your feelings? Did you feel pain from being struck by weapons fire? Was it more or less? Is it based on human physiology or your own ship-based physiology? How did-?"
Ben: "Yo, Stretch! Give her some room, eh?"
Reed: "Huh? Oh, I'm sorry. I got carried away."
Enterprise: Patiently "It's all right... This is all very overwhelming for me, too."
Reed: "Er, of course. I must say though, the transformation is incredible. It's not magic, it's reality editing technology! How incredible!"
Peter: "So, who would create a ship girl out of the Enterprise, anyway?"
Tony: "Better question, Stonewall: Who would create multiple shipgirls out of dozens of old warships?"
Reed: "What? Come now! The manufacturing requirements for this kind of transformation are astronomical! The odds of there being multiple beings of this nature are-!"
Tony calls up the local news on the nearby monitor. Multiple women and girls with naval weapons and equipment were shooting at eachother around Hawaii, North Carolina, and multiple other locations.
Reed: "... Ah. I may have misplaced a decimal point..."
Peter: "Ya think?"