Crossover Shipgirls: Building a Dimensional Empire from Scratch

EVA World.

On the border between Kanagawa and Shizuoka Prefectures, nestled among the Hakone Mountains, stood a sprawling city.

Unlike ordinary human settlements, its skyscrapers were not merely offices or residences but heavily armed fortresses equipped with an array of defense systems. Inside were stockpiles of supplies—power generators, ammunition, and heavy weapons—all meticulously maintained and ready for war.

This was Tokyo-3, a true fortress city.

Years ago, the rising global sea levels had submerged the original Tokyo, forcing the government to relocate to Tokyo-2. At the same time, this new city was built to research and defend against mysterious beings known as Angels.

”Warning!”

”At 12:30 PM today, a state of emergency has been declared across the central Kanto region, with the eastern sea zone as the epicenter.”

The blaring broadcast echoed throughout the city.

”All residents, please proceed immediately to designated shelters. Repeating—at 12:30 PM today...”

By now, the surface of Tokyo-3 was eerily deserted.

The empty buildings loomed over abandoned cars and silenced streets. Buses, subways, and every form of transportation had ceased operation.

A heavy, oppressive silence hung in the air—clear evidence of a hasty evacuation.

Only at the outskirts could one still see lines of armored forces stationed along the coast—tanks, APCs, and anti-tank cannons lined up, all weapons aimed toward the sea.

The soldiers stared nervously toward the distant ocean.

Whoosh—

From high above, one could make out an enormous humanoid figure emerging from the deep, striding steadily toward the city.

”Open fire!!”

Boom-boom-boom-boom—

A storm of artillery shells rained down, raising columns of spray across the water. Yet the colossal being advanced unhindered.

Splash—

As it reached the shore, the soldiers finally saw what they were up against.

A humanoid creature—towering many times higher than the city’s tallest skyscraper—its body mostly black, its head located where its chest should have been, and strange bone-like structures protruding from its joints.

Grotesque. Terrifying.

”Deploy all forces! Stop it!!”

The commander’s voice roared over the comms.

Gunships and fighter jets scrambled into the air, targeting the entity. Vulcan cannons unleashed streams of fire capable of tearing through steel, while dozens of missiles streaked toward the Water Angel.

BOOM—

BOOM!!!—

The explosions echoed across the city, smoke and shockwaves rolling outward—but all the attacks were halted by an invisible field surrounding the creature. The Water Angel was completely unscathed.

Crack—

From its elbow extended a glowing white spear. With a single swipe through the air, the jets above were sliced apart like butter.

”How... how is that possible?!”

In the command center, the officers stared in horror as the Angel rampaged through the city.

Even the United Nations’ most advanced weapons were useless against it. Tanks and armored vehicles were nothing but paper before its might.

Even when they deployed their most powerful armament—the N² aerial mines, comparable in yield to tactical nuclear weapons—the effect was negligible, slowing it only slightly.

”How can this be?! None of our weapons are working?!”

”Damn monster!!!”

...

Meanwhile—

Beneath Tokyo-3, under layers of reinforced steel plates, six kilometers below ground, lay a vast underground complex.

Everywhere one looked were armed guards, control stations, and research labs bustling with personnel.

At the main entrance, a red emblem was etched into the wall: NERV.

A secret special agency under the Human Instrumentality Committee, NERV’s purpose was the development and deployment of Evangelions—as well as the research and annihilation of Angels.

Inside one of the massive underground hangars, a colossal humanoid machine rested in maintenance—a towering figure painted in violet, most of its body submerged in a strange fluid, only its head exposed.

”What... is this?”

A boy in a white shirt stood on a catwalk, staring in disbelief at the giant before him.

”This,” answered a nearby officer, ”is the ultimate general-purpose humanoid weapon—Evangelion Unit-01.”

”It’s humanity’s final trump card—our ultimate weapon against the Angels, built to defend Tokyo-3.”

”Oh...”

Shinji Ikari stared blankly at the towering Unit-01.

”So... this is Father’s work too?”

In his memory, his father had almost never been there for him. For him to summon Shinji so suddenly to Tokyo-3 could only mean something urgent.

”Yes.”

From the platform above, a man in uniform appeared.

Gendo Ikari—Commander of NERV.

”Deploy.”

He gave a cold, concise order.

”Shinji Ikari, you will pilot Unit-01.”

”Defeat the Angel.”

”W-What?!”

”Father, you’re asking me to pilot that thing... and fight that monster?!”

Shinji’s voice trembled with fear and disbelief.

For a boy his age, being told to shoulder humanity’s fate and face an incomprehensible terror was too much to bear—especially from a father he had long been estranged from.

”Why now?! You didn’t need me before—so why now?!”

”I called you because you’re needed. Nothing more.”

Gendo’s tone was devoid of emotion. He watched his son’s breakdown with an expression as cold as stone.

”If you can’t do it, then leave.”

His voice thundered across the command room. Then, without hesitation, he turned to the comm system.

”Rei Ayanami. The substitute pilot is useless. You will fight.”

”Yes, sir.”

Just as Gendo began his carefully crafted psychological manipulation—intending to crush Shinji’s resistance and make him willingly pilot the EVA—

Suddenly—

BOOM—

The ground trembled violently.

”What?”

Gendo frowned and looked up in confusion.

A brash voice crackled through the comm channel:

”You don’t wanna let me pilot the EVA, huh?! Don’t waste it!!!”

”First Squad—go seize NERV! I’m taking down that Water Angel myself!!!”

”???”

”Who the hell is that?!”

Everyone in the control room froze.

NERV’s existence was top secret. Its internal channels shouldn’t have been this easy to breach—and whoever it was seemed to be watching them in real time?!

Whoosh—

The operators quickly projected the surface surveillance feed onto the main screen.

Fwoosh—

From the clouds, a massive red-and-white humanoid machine descended like a missile, wings spread wide, leaving trails of fire in its wake.

It was even larger than the Angel.

Its design vaguely resembled an EVA, but its armor was entirely metallic—one hand wielding a shield, the other a spear.

Behind it, an entire host of Angeloids descended, armed with weapons of every kind.

Compared to the so-called ”Water Angel,” these looked far more like true angels.

BOOM—

The crimson mecha landed with a thunderous crash, scattering dust and debris.

”Ah—ha!”

Gudako laughed wildly inside the cockpit, thrilled beyond measure—finally getting to pilot something that felt like a Gundam.

”Another Angel?! Or...”

”No—no, wait!!!”

”Retreat!!! Everyone fall back!!!”

The human forces, stunned by the descending mecha and its angelic army, panicked and fled in terror.

”Alright then—let’s see what you’ve got.”

Gudako’s mecha—Strelizia—charged straight at the Water Angel.

”...”

The Third Angel sensed hostility. Its arm extended, forming a glowing spear aimed directly at her.

BOOM—!

The attack slammed into the mecha’s energy barrier, producing ripples of blue light—but failed to pierce through.

”That all you got? Even Tohru hits harder than you.”

A grin spread across Gudako’s face.

CRACK!!

Strelizia thrust her spear forward—piercing straight through the Angel’s chest.

The creature’s AT Field shattered instantly, powerless before the overwhelming force.

Then, as if to flaunt her victory, the mecha lifted its spear high into the sky—impaling the writhing Angel.

The Angel’s massive body weighed nothing in her grip.

”Boom.”

BOOOOM!!!—

Energy surged through the spear, detonating within the Angel’s core. The explosion tore it apart, scattering its remains across the ruined city.

”See? I told you. Way better than Chaldea’s magecraft.”

Gudako nodded in satisfaction.

”Record this—send it to Dr. Roman. Tell him times have changed.”

”Ah...”

The remaining human soldiers could only gape in disbelief.

Deep underground, Gendo Ikari stood frozen, eyes wide.

The first stage of his Human Instrumentality Project had just gone completely off the rails.

What the hell is this?!

Was that supposed to be an EVA? Why had he never heard of such a thing?!

And since when were EVAs this ridiculously overpowered?!

”Who are you?”

Suppressing his shock, Gendo opened a comm link to the mysterious intruder.

”I am Ritsuka Fujimaru, from Chaldea. By order of the Commander of the Starsea Empire, I am here to conquer this world.”

”So be good and surrender already.”

”???”

”Ah?!”

...

”What the hell is going on here...”

Deep beneath Tokyo-3, NERV headquarters had descended into temporary chaos.

From the classified briefings and reports they had, everyone understood that the Angels were humanity’s greatest enemies in this era. Born from Adam, they represented alternate evolutionary forms of humanity—each one seeking the extinction of mankind.

But now, what were those so-called Angeloids filling the sky—and that massive red-and-white machine? What was happening?

Many personnel mistook Strelizia for another Angel, believing they were facing two simultaneous threats.

”...”

Gendo Ikari’s expression remained composed, but inwardly, his mind was in complete turmoil.

For the sake of the Human Instrumentality Project, he had planned everything meticulously over years—perhaps decades. According to his script, he would soon bring out the injured Rei Ayanami, and Shinji, overcome by guilt, would pilot Unit-01 to defeat the Angel.

Then, step by step, he would manipulate events until Adam and Lilith merged, achieving godhood—and fulfilling the ultimate goal of the Human Instrumentality Project.

And now... some giant Gundam from the sky wanted to conquer the world?!

”Alert all divisions. Seal the surface access tunnels. Deploy defense units.”

Clang—Clang—

The layers of reinforced gates surrounding NERV headquarters slammed shut one by one.

”Father, what’s... happening?”

”The mission has changed. You’ll pilot Unit-01 and intercept her.”

Gendo pointed at the screen showing Strelizia.

”Ah?!”

”You’ve got to be kidding me!”

Shinji was dumbfounded.

A moment ago, he was terrified at the idea of fighting the Water Angel—and now they expected him to face the thing that one-shotted it?!

”No way... no way! How could I possibly—me, alone—fight something like that?!”

Shinji’s voice cracked as pure fear seized him.

”The EVA is humanity’s ultimate weapon. You are the Third Child—the only one capable of piloting Unit-01.”

”Humanity’s in danger. Get in the EVA and stop them.”

Gendo’s command was delivered with his usual cold detachment.

”Or... would you rather let her fight in your place?”

The medical team rolled in a stretcher. Lying on it was a pale girl with short blue hair and crimson eyes—her body wrapped in bandages, one eye covered, an IV drip attached to her arm.

”Rei Ayanami. You will pilot Unit-01 and intercept those targets.”

”Understood.”

She struggled to sit up, coughing weakly, her voice calm and devoid of emotion.

”Ah...”

She tried to climb off the stretcher but could barely move—each breath shallow and labored, every twitch of her muscles a battle against pain.

”I...”

Shinji froze.

To let an injured girl go out and fight in his place?

He wasn’t even sure Rei could make it to the cockpit, let alone survive in combat.

But to step into the EVA himself, to face that unknown enemy—it felt utterly impossible.

Fear, guilt, and confusion tangled together inside him, leaving his face twisted in anguish.

”I can’t... I can’t run away...”

”But that thing—there’s no way I can fight something like that...”

As he struggled internally—

BOOM—

The ground shook again.

”Hey, hey, hey! Moral coercion isn’t cool, you know?”

”Just hand over that EVA already, would you? If you don’t surrender, I’ll come down there myself!”

Gudako’s cheerful voice crackled over the comm channel, full of energy.

”Trying to guilt-trip your kid into dying for you? You seriously think that toy can beat me?!”

”!?”

Gendo’s eyes widened in shock. The intruder could see and hear everything happening inside NERV in real time. Every word, every movement—they were being watched.

”All units, battle stations!!! Fortify all entry points!!!”

The trained soldiers grabbed their weapons and quickly assembled.

Even though they were deep inside a fortified underground base, the illusion of safety didn’t last long.

Vrrrrr—

Zzzzzzt!!—

The sound of thermal cutting echoed from above.

Over NERV headquarters lay twenty-four layers of special composite armor—its defenses surpassing even those of world leaders’ bunkers. It could withstand multiple direct nuclear strikes.

The Angeloids didn’t care.

They locked onto their target and, with concentrated laser fire, began cutting through the ground as easily as slicing butter.

No amount of terrestrial engineering could stand against the weaponry of an interstellar civilization.

Zzzzz—

NERV’s defense troops could only stare in horror as molten metal rained down and a massive hole tens of meters wide opened above them.

Boom—CRASH!!!

Strelizia led the descent, spear in hand, blasting through the tunnel, followed by thousands of Angeloids roaring in behind her.

The NERV defense units were instantly annihilated. With the help of the Sophons, there wasn’t a single corner of the base the Angeloids couldn’t strike.

BOOM—

Strelizia landed before the command staff, smoke and dust scattering in waves.

Everyone was stunned. The machine was even larger than Unit-01. If the EVA could be described as a divine biomechanical being, then Strelizia was the pinnacle of technological evolution—a fusion of machinery and science from a galactic civilization.

Every detail of her design, from the alloy plating to the modular weapon systems, radiated futuristic power.

BOOM—

As they stood frozen, another figure dropped through the tunnel—a girl holding a crowbar, a single long ahoge swaying atop her head.

”Oh? Gundam versus Gundam? Guess I should change forms too!”

Nyarlathotep struck a pose.

Whumm—

Her body lit up, encased in a black combat suit as plates of armor materialized across her shoulders, chest, and legs—complete with a stylish belt.

Her head was soon covered by a full-face helmet resembling a Kamen Rider’s, red light glowing from the eyes.

”What... what the hell?!”

Gendo Ikari and the NERV staff were utterly dumbfounded. A Kamen Rider? Here?!

”Behold—the Crawling Chaos ever lurking beside you, Nyarlathotep, has arrived!”

Wham—Crack!

In just a few moves, Nyarlathotep had floored the remaining guards. Between getting to cosplay and beating people up, she was having the time of her life.

”Who are you people?!”

Gendo barely got the words out before—

Gudako waved her hand dismissively.

”Take them down.”

Whoosh—

In the blink of an eye, every NERV staff member was pinned to the floor by Angeloids, unable to move.

Their speed far exceeded human reaction time.

”Hmm...”

Gudako hopped out of Strelizia’s cockpit, stretching her arms.

She was thoroughly enjoying herself—there was something addictive about playing conqueror.

”Take her back for treatment,” she ordered.

An Angeloid gently lifted the unconscious Rei Ayanami—knocked out by shock—and carried her toward the starship.

Then Gudako turned to face Gendo Ikari.

”You pathetic native... You still think you can challenge Strelizia? Please. Fighting Unit-01 and Shinji wouldn’t even be satisfying—it’d be like kicking a puppy.”

”...”

Pinned beneath an Angeloid, Gendo strained to look up at the strange girl who had turned his entire world upside down.

His eyes were full of confusion and disbelief.

”Who are you? Where did you come from? What do you want?”

”I literally just told you, didn’t I? Are you a goldfish? Memory lasts seven seconds, tops?”

Gudako waved her hand in front of his face, sighing.

”Anyway—we’re here to conquer this world. Angels, Adam, Lilith, whatever—you name it, we’ll clean them up.”

”Of course, this world will become part of the Empire afterward. So behave, okay?”

”???”

Tilting her head, Gudako studied the notorious mastermind of the EVA world.

”Normally, we’d vaporize any stubborn or defiant resistance...”

”But you—you’re clever. Scheming, manipulative, ruthless. That kind of brain might still be useful.”

In the original timeline, Gendo Ikari had been a master of deception—joining NERV and SEELE only to use both for his own ends, manipulating everyone and discarding them without hesitation.

”?”

Gendo frowned.

”You’re... recruiting me? Who exactly are you?”

He assumed these mysterious invaders shared his interest in the Human Instrumentality Project.

”Yup. The Empire always needs talent like yours.”

Gudako clapped her hands.

”There’s a position waiting for you in the Synaptic Lathe. You can pursue your grand plans there to your heart’s content.”

”Take him away. There’s a prison here, right? Lock up the rest of the stubborn ones too.”

”???”

Gendo was dumbstruck as the Angeloids dragged him away.

In previous conquests, the Starsea Empire had simply executed anyone who refused to surrender.

But since the advent of the Synaptic Lathe Project, the Expeditionary Forces had discovered a more practical use for their enemies—recycling them for residual cognitive output.

Even the smallest contribution was still something.

”By the way,” Nyarlathotep said, tilting her head, ”did the Commander actually say how to deal with them?”

Gudako waved dismissively.

”Relax. He’ll back me up. Nobody understands the Commander better than I do—we’re morally aligned, trust me.”

—

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