E7 Part 5: Category 5

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Central Dogma. Command Center.

It occurred to Shinji for the first time just how little he'd thought about his father over the last few months. There'd just been so much happening since he'd met the Doctor -- day after day, week after week. Looking back on it all, it felt like he'd scarcely had the chance to sit down, let alone contemplate the past.

Strange, he thought as he felt the color drain from his face, just how easily it all came flooding back to him now...

A dozen-man security team quietly filed into the room past Shinji. They spread out and took position around the Doctor.

"Oh. Oh, of course." The Doctor narrowed his eyes. "I never did catch your name, did I?"

"Gendo Ikari." Father pushed back his glasses. "I command this organization."

"Uh-huh. So running into you at the park -- you planned that, then, did you?"

"I find intelligence reports only go so far," Father said. "One must sometimes look into matters personally. Wouldn't you agree?"

"Yeeaaaahh, that's very interesting and all -- but there's still the small matter of the being you're torturing downstairs as we speak!" The Doctor stared the commander right in the eye. "Care to explain yourself, sah? 'Cause right now, I don't see a single reason I shouldn't shut down this whole operation this very minute."

Next to Shinji, Asuka snorted. "Oh, please," she muttered. "Like he could do that..."

Shinji didn't say anything. He felt sick -- actually, physically sick -- to his stomach. This couldn't get any worse. There was no way Father would ever forgive such an insult. He glanced at the security team. They hadn't drawn their weapons yet, but each one had a clear line of fire to the Doctor.

What was Shinji going to do? What could he do?

He found himself holding his breath...

"Fine," Father said.

... wait, what? Even Vice-Commander Fuyutski looked confused. Shinji saw him shoot a surprised glance at Father, as if to ask really?.

"Everyone under the rank of Lieutenant is to clear the room immediately," the commander said. "You are to close and lock the doors until ordered otherwise. The pilots may stay."

The majority of the command staff migrated away. The Doctor stood his ground, not breaking eye contact with Father for so much as a second. Misato stayed as well, her arms crossed, her hand still clenched around the wind-up radio. In the end, only a relatively small number of people remained, including the security team, Lieutenant Aoba, Maya, Ritsuko, Asuka, Rei and Shinji himself.

The doors slammed shut.

"This information is highly classified," Father said. "It is not to leave this room under any circumstances."

"Just get on with it," the Doctor snapped.

"We call the entity you saw Lilith." Father adjusted his glasses. "She crashed onto this world approximately sixty-five million years ago. In her wake, she remade the entire biosphere in her image. Every extant species on the surface of the planet is descended from her in some way. Moreover, every living organism on Earth contains a small, self-replicating piece of her substance within its genetic code."

"If that's true, she'd be the source of all life on Earth." The Doctor furrowed his brow. "So why imprison her?"

"As you are still alive, I presume that none of you attempted to touch her." Father glanced at Rei. She shook her head. "Any organic material that comes into contact with her flesh is immediately absorbed into her body as it reintegrates the fragments of her matter within the Lilith genes. This appears to be an automatic reflex. Every piece of intelligence we have -- every experiment, every study -- suggests that, should her body merge with a sufficiently powerful energy source, this effect will be extended planet-wide."

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