So this is a novelization of an RP that took place over IRC about five hours ago. Uh, I guess I'll just get right to it.
The cast:
Seele France/Francois = Hoshikawa-kun
Misato Katsuragi = Seele00TextOnly
Shinji Ikari = Anti-Goth
Rei Ayanami = Seele00TextOnly
Asuka Langley Soryu = Seele00TextOnly

Part 01: Bad News, From God


“Commander Ikari. You are hereby relieved of your duties— all of them.”
Amidst the light of the helicopters that day outside NERV HQ, all Gendo could see was the man's glasses, glistening in the artificial light.
“...Who in hellfire are you?”
“Hellfire...?” A full set of glossy white teeth now shown alongside those glasses, “Exactly.”


Misato approached the door to the Commander's office, the nasally announcement ringing out over the public address system.
“Attention! Az of 6:29 AM today, I am your, ou you zay...Commandant!”
A new Commander? Admittedly, she'd only just checked her inbox and found the pile of notifications and official statements sent weeks prior, but even had she known of this a month in advance it would have been shocking.
“Commandant Ikari haz been apprehended by ze authorities on charges of...disorderly conduct, and abuse of hiz powers.” SEELE France spun about in the swivel chair that had once belonged to Gendo Ikari, dangling the PA system microphone about his finger, “The full authorities of NERV are now vested in moi.”
In the floor below Rei Ayanami's eyes turned skyward, her features downcast. She had not been informed of this.
“Hello sir!” Misato entered the office after a single customary knock, her arm coming up in a strict salute, “Misato Katsuragi, Tactical Operations branch.”
“You may address me, workerz and employeez of NERV, as Commandant Francois. That is FRAN-SWAH, if you pleaz! Good day, everybody, I look forward to working wiz you all!” Francois slouched back in his chair as he shut off the microphone, “And hello to you too, Major Katsuragi.”
Commander...Francois?!?!
“You are such a pretty little thing, Major.” Francois set a foot upon the floor as a smile broke out beneath his long nose, pushing up his spectacles, “I cannot believe my predecessor dumped so much of ze...paperwork, on you. Pleaz, rest assured zat in ze future, these base duties shall be, ah...allocated to more suitable personnel. Now...where are ze Children?”
“Er...I'll call them up right away. One of them is away today, actually, though...” Misato hurriedly turned her attentions to the boxy gray NERV cellphone, paging the two as quickly as she could manage.
“Oh my. So sad it is not here, but zese things do happen. I will meet ze missing Child when it is appropriate.”
“Yes sir.”
Where are they...? Misato considered in the silence. She had become more and more distant from Shinji since Asuka had arrived.
“Zey must have such difficulty getting here on zeir scrawny little legs. Such unfortunate Children.”

“...? What was that all about?” Shinji inquired to the girl across from him, looking disconcerted by the announcement. He couldn't understand a word of what the new 'Commandant' had been saying.
“The commander has been apprehended.” Rei's brow furrowed in concern.
“...?! What? Father?!” Shinji came up from his sitting position, immediately straightened out by the news, Oh...right. “Er...i-it's alright, Rei...I'm sure it's just a mistake...”
“...Mistake.” Rei's eyes traced the tile down, falling to stare at where the floor met with the wall.
Shinji was jarred by a sudden vibration in his pants, reaching down and quickly opening the phone to be greeted by Misato— in that business tone that had beset her voice of late.
“Please come to the Commander's office.” Click. Beep. Beep.
“...I think we're supposed to...go meet the new Comman—“ Shinji turned to look at Rei, but the girl was already on her feet, calmly proceeding to the stairs, “...er. Ayanami...!”
Shinji quickly made to follow her, but Rei had stopped at the sound of his voice, now turning to regard him with the same composed stare once reserved for his father.
“...Yes?”
“Sorry, I...um...” His tongue tripped in his mouth; the words wouldn't come.
“...We must go.”
Shinji nodded, anxiety pushing his step as he followed Rei up the stairs and to the solemn office door.

“Ah! And 'ere they are!” Francois clapped his hands together with a smile, rising from the seat.
Rei took her place facing the Commander with her usual expression, Shinji appearing far less composed before the frenchman.
“...Hello, sir.” Shinji bowed low, Francois consulting the documents on his desk carefully.
“Mmm. I have heard much of you, Childrenz. You, Shinji Ikari...your exploitz are well known to me. I applaud your skill and prowess in battle. And you, Rei Ayanami—you are ze former Commandant's...fille?”
I wonder what the Commander did... Misato's arms tightened in a fold as she moved to stand at the side of the room, sweat beading on her neck. These events were all happening very quickly for an organization that normally only moved so fast in an Angel attack. ...or didn't do?
“Th-thank you, um...Commander.” Shinji bowed once more, Fille?
“I am sorry, I do not understand.” Rei did not pretend to have any mastery of French; she knew only English and Japanese, as was required of her.
“That iz to say, you are hiz daughter.”
Wh-what? Misato had to exert restraint not to let her jaw fall wide.
“I am sorry, you are mistaken.”
“Oh, my. Could you tell me, Ms.Ayanami, what year you were born in?”
“2001.”
Ikari, what iz that damn fool doing...I must know! Rei iz nto part of this! Not...in any...WAY! Secretly Francois was exerting a noticable pressure on the documents, infuriated by the dead ends he had been struck with so soon. Gendo was far too clever for his own good. “I zee. Yes, zis would match up. What parents were you born to?”
“I...” Rei fumbled, taking a step back, “...do not know.”
“Ah! Ce tragic! Poor little object.”
Rei froze up, attempting to stand stoic— yet somewhere she felt a pang in her cold skin, a break in the fragile shell she'd built.
“You three muzt have...so many questionz. Plz, take zis time to ask them of moi.”
Misato stared at Shinji for a moment, noting the clenched fists— and, hazarding a guess at his thoughts, speaking up. “What do you know about Commander Ikari's situation?”
“He iz presently dueling upon ze field of honor...er...” Francois' mouth twisted unpleasantly, before he corrected himself, “He haz been apprehended for questioning regarding his recent actions. He has recently infringed upon hiz powers considerably.”
“That's terrible to hear, but I'm certain the Commander would have done nothing of the sort.” Misato insisted, more out of loyalty than any real love for her boss. He was a slavedriver who dumped too much paperwork on her, but she trusted this 'Francois' even less than Gendo.
“Major Katsuragi, are you aware of what is present in the, ahem...” Francois appeared delighted by Misato's objection, his smile positively catlike, “Basement?”
“I have no idea what you're talking about, sir.” Misato replied quietly.
“Good, because nothing iz there now. Suffice to say, I cannot zuggest that Commandant Ikari will be released anytime soon.”
“W-why would you think Ayanami is my—“ Shinji finally burst out, looking up and finding his words caught in his throat as he saw the man's twisted face, “...er.”
“...Yes sir.” Misato nodded, not sure what else to say. Rei certainly didn't appear any more or less sullen by the news, but Shinji was far more befuddled by Francois' words.
“Mr. Ikari,” Francois looked down to speak with Shinji directly, “I regret to inform you zat you and Ms. Ayanami share a great deal of ze facial structure. And there are...other, reasons for me to suspect such things. Your fazer has a great many mysteries surrounding him.”
“What?!”
“Do you see now, why we are questioning him?”
“I...I guess so, sir...”
“Well, I digress.” Francois sighed, feeling the pressure of the Major's gaze. “Ms. Katsuragi, where is ze Second Children?”
Shinji snuck a glance at Rei, beginning to wonder just what made Francois assume them to be siblings.
Well, they do seem a little...but that makes no... Misato cringed at the pair, Or could it...
“She's been out an amusement park with Kaji all day. It's too great a distance to call them on such short notice...So, there you have it. I'll bring her to you as soon as possible.”
“Ah. Pity. Oh well, if you have no more questionz, I have a number of other personnel I must acquaint myself with!” At his dismissal Rei and Shinji both turned to leave, Shinji setting a pair of earbuds in his ears. “And, Ms Katsuragi...”
“Yes, sir?”
“Are you aware of any...” Francois' voice had become abruptly hushed, “Strange transactions, between Commandant Ikari and Doctor Akagi?”
...Ritsuko?
“No, sir.”
“Ah, I see. Please alert me to any strange activities you see. And good work in ze previous Angel battles, I am highly impressed with your creative tactics. Dismissed!”
“Thank you.” Misato saluted, and promptly turned on her heel, the door clicking shut behind her as she departed the office.
Francois leaned back in his chair, propping his feet on the desk as a handheld recording device came alive in his gloved fingers.
“Kuh. Ze Commandant Ikari was veeeery careful in how he conducted hiz operations, but he will not last long against Chairman Keel. I have found no one wiz knowledge thus far of the shared bank account between Ritsuko Akagi and Gendo Ikari, nor what became of the artifacts in Central Dogma. The scenario has deviated significantly...but I am confident we can eventually proceed as planned, with...some accommodations for these changes. End recording!”
At this Francois resumed spinning in the chair that had once belonged to Gendo Ikari, relishing in the polished leather.
“He was very careful indeed. This...was not on ze list of things paid with NERV's budget.” Francois' fist slammed on the arm of the chair, sinking into the steep cushion, “Damn it, I need one of zese!”