Crossover Shipgirls: Building a Dimensional Empire from Scratch

”Commander, we’ve discovered something rather interesting from our previous spoils.”

At the EVA world’s research center, Setsuna arrived at a deep underground testing facility. A group of little lolis from the Life Sciences Division, led by Muroto Sumire, were bustling about with busy determination.

Normally, most research work would be conducted back in the Starsea Empire, after the expedition teams brought back their spoils. The home facilities were far better equipped.

However, the EVA world was special. Projects such as the Human Instrumentality Program could only be carried out here—after all, humans from other worlds weren’t descendants of Lilith.

”We’ve extracted cellular samples from Lilith and successfully cultivated them. We’ve done the same with Adam,” Kayo Senju explained as she led Setsuna through the facility.

In the heavily guarded lower hall, Lilith’s massive body floated in midair, suspended by a containment field, the Spear of Longinus still impaled through its chest.

Beside it was another figure—larger, radiant, and also restrained by powerful force fields, with a similar spear lodged in its torso.

”This is... Adam?”

Setsuna blinked.

”Yes. Using the Adam embryo recovered earlier, we extracted cells and regenerated its body,” Kayo Senju nodded.

”Adam possesses the Fruit of Life, the progenitor of the Third through Sixteenth Angels. Though its soul has long since dissipated, its biological structure holds immense research value.”

”Uh... if you wanted to, Commander, we could transplant Adam’s cells into your body, then merge them with Lilith’s soul vessel—Unit 16—and you could complete the Human Instrumentality Project instantly.”

As she spoke, Muroto Sumire’s gaze drifted toward Rei Ayanami.

”Stop. Isn’t that exactly what Gendo Ikari tried to do? Don’t bring up such rotten ideas.”

Setsuna waved his hand dismissively.

With his current level of power, he could easily fulfill every requirement for Human Instrumentality through sheer force—but he had no interest in turning humanity into orange juice.

”I figured you’d say that. Just a joke.”

Muroto shrugged lightly.

”Still, although these two entities aren’t gods in the conventional sense of ’rule-manipulating, world-creating deities,’ we did manage to extract something from them—something resembling divine authority.”

”Oh?”

Setsuna’s eyes lit up. ”Go on.”

”The authority to create life.”

Muroto led him deeper into the facility.

At the center of the next lab stood a massive cylindrical tank filled with a thick, golden-yellow liquid.

Several research lolis and Angeloids worked busily around it—extracting small samples and placing them under microscopes, operating delicate instruments with focused precision.

”This is LCL—also known as the Sea of Life. It originates from Lilith’s body and is used within EVA units. It represents the primordial state of all life.”

Setsuna nodded in understanding.

In the EVA world, all life shared the same origin—souls residing within a vast ocean of Lilith’s blood.

This was, in fact, the ultimate goal of the Human Instrumentality Program.

”When we first began studying this ’Sea of Life,’ we kept asking ourselves one question,” Muroto continued.

”Since all life on Earth evolved from it and will eventually return to it... could we not use this same medium to create new life?”

Her words left everyone momentarily speechless.

”Create new life? From this pool of orange juice?!” Gudako’s jaw dropped.

”Yes,” Muroto replied calmly. ”Life on Earth once evolved from the Sea of Life eons ago. We can do the same.”

”In theory, the Sea of Life can give birth to all forms of existence—animals, humans, or even entirely new species we’ve never seen before.”

”We tried simulating biological evolution using it, and... it turned out to be far simpler than we expected.”

”???”

”What kind of creatures can you make now?” Formidable asked curiously.

”Single-celled organisms—for now. We’ve only been studying this for a short while, so that’s already an incredible achievement, alright?!”

Muroto Sumire adjusted the microscope slide on the experiment table.

”...”

Setsuna fell into thought.

Creating a living organism from nothing was something entirely different from natural reproduction. The leap from zero to one was monumental, but once achieved, going from one to one hundred was easy.

”So basically, a reverse Human Instrumentality Project? Not bad. Just... don’t create any higher-intelligence beings for now.”

”Understood~”

Muroto led Setsuna into the next laboratory.

”Adam possesses the Fruit of Life. The beings born from it—the Angels—are far stronger than humans. They need no food or rest, and they possess infinite lifespans. In a sense, they are perfect lifeforms.”

”We’ve used Adam’s cells to clone and create another form of life—a synthetic Angel.”

Following her finger, Setsuna saw a strange creature confined within a transparent chamber.

It was disk-shaped, with four sharp, jointed limbs extending from its sides. Like other Angels, its appearance was bizarre and alien, floating quietly in the limited space.

”Uh... this Artificial Angel 4A doesn’t look too smart.”

Setsuna tilted his head slightly. The Angel didn’t seem to possess intelligence.

”Exactly. Angels are far stronger than humans, but they act purely on instinct. They lack the capacity for communication, reasoning, or the use of tools.”

”That’s the limitation of the Fruit of Life. The descendants of Lilith and Adam are inherently incomplete beings.”

”Unless we merge the two—but that would trigger the Third Impact, and the Earth would be doomed.”

Muroto spread her hands helplessly.

”...”

To be fair, creating a new lifeform from scratch was impressive. But Setsuna was more interested in its practical use.

”So... we can create Angels ourselves now? What are they good for?”

”Uh...” Muroto thought for a moment.

”Two main things. First, we can extract S² Engines from them—the same ’Fruit of Life’ organ that powers the Angels.”

”The process is complicated, and production won’t be high, but its applications are vast.”

”If we implant an S² Engine into an EVA, it’ll gain the Angels’ regenerative ability and limitless energy.”

”For humans, the effects would be similar—uh, theoretically, they’d become self-sustaining, sleepless, immortal... ultimate perpetual workers!”

”...”

Setsuna sighed, pinching the bridge of his nose.

”The Fruit of Life sounds incredible, but why does it sound so depressing when you put it that way?!”

”That’s the second thing,” Muroto continued. ”We plan to use the Artificial Angels as living perpetual engines—let them mine, process materials, maybe even work in hazardous environments...”

”Then I realized—if I grafted the Fruit of Life onto myself, wouldn’t that make me the ultimate eternal employee?!”

Her expression went blank with despair.

”...Your imagination and level of resignation are truly awe-inspiring.”

...

The main research efforts in the EVA world were divided into two major projects: one focused on the EVA mechas themselves, and the other on Lilith, Adam, and the Fruits of Wisdom and Life—along with all topics related to Human Instrumentality.

After touring the facilities, Setsuna confirmed that most of the research had already reached a satisfactory level. The rest could be managed by establishing a permanent research outpost for ongoing study.

Before leaving, another thought crossed his mind.

”Come with me.”

He took Rei Ayanami and several Angeloids, following Sophon’s guidance to a hidden underground medical facility beneath NERV.

Inside the secluded chamber were numerous advanced medical machines—far beyond anything from the pre-space era—including what seemed to be a consciousness-transfer device.

On one side stood rows of cylindrical pods, each about human height, filled with nutrient fluid.

Inside each pod floated a girl—identical in face and figure to Rei Ayanami.

Their eyes were closed, suspended motionless within the liquid.

”Ah...”

For the first time, Rei—normally expressionless—looked stunned.

”This is... me.”

”Even if I die, it doesn’t matter. They’re all... me.”

The girl’s voice was calm and emotionless.

She was a clone born from Lilith’s cells, existing solely as a vessel for Lilith’s soul.

Even if she died, NERV would simply transfer the soul into a new clone.

The countless identical bodies before them were, essentially, her ”backups.”

Rei Ayanami had already died once. The Rei standing here was the second generation.

Even if the soul transfer didn’t preserve her memories completely, she faintly understood her fate.

”No—you are the only one.”

Setsuna gently brushed a strand of her hair aside, then waved his hand.

The Angeloids quickly moved into position, using high-energy lasers to destroy every clone one after another.

The soulless shells were reduced to ash within minutes.

”Ah...”

At first, Rei looked confused.

Then she suddenly realized what had happened.

Setsuna had destroyed all the other copies—leaving only her.

”The only one.”

”What does... ’only’ mean?”

She lowered her head, repeating the words softly to herself.

For someone who had always lived in cold detachment, for the first time, she felt a faint warmth stirring within her heart.

”You are Rei Ayanami—not a vessel, not a tool for the Instrumentality Project. No one can replace you. In this world, you are unique.”

”From now on, live well in the Starsea Empire.”

Setsuna gently cupped her cheek and met her gaze with quiet sincerity.

”Ah...”

Rei’s expression grew complicated.

No one had ever said such words to her before. A faint blush appeared on her pale face.

”...I’m sorry. Thank you. I don’t know how to respond to that.”

”Just smile. That’s enough.”

”...”

Rei tilted her head slightly and gave Setsuna a soft, genuine smile.

”Thank you, Commander.”

—

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