"Ikari's asset." The one asset they were actually talking about is Kaji. Plus, "terminate". In canon, Fuyutsuki and Ritsuko were captured; only Kaji was killed.

Though if Kiel (I refuse other spellings) is speaking in general, it could also be Fuyutsuki, Ritsuko or Rei. Unless they somehow learned it earlier in A&T and I have forgotten that, they don't know yet what Rei is. So to them, she might simply be "Ikari's pet pilot", i.e. asset (otherwise I think they'd refer to her by her Lilith connection). Though if they are speaking about "asset" in general, then I would say the most likely bet is Fuyutsuki, because well, canon.

I feel like they'd talk about EVA-01's core in much different terms. For one, they probably know its importance to Gendo, more than just an "asset", and second they would refer to that unit with another name, seeing how central it is. Plus I'm not sure you can actually change EVA cores. The units seem to be built around them. If you could, well, then you wouldn't need to recruit the daughter of one of your chief engineers in a hurry just it was her who made the contact experiment. Then you could go about this much more planned. So I very much think EVA cores are non-exchangeable.

So my order of likelihood: Kaji, Fuyutsuki, Ritsuko/Rei.
 
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"Ikari's asset" could mean a lot of things, come to think of it. Rei is the main candidate, but Kaji is a contender too. They might (but probably don't) mean Shinji, even...

EDIT: Or Fuyutsuki.
I'm pretty sure it means Kaji. He was, after all, mentioned by name as the guy spearheading the housecleaning operation for Gendo.

Ritsuko wouldn't really fit, since she's too important for the Evangelion program and defeating the final Angels (which is important to SEELE, since if the Angels win, they all lose).

Fuyutsuki is...not really a practical threat to SEELE. He's just Gendo's underling-in-chief. He's not an active threat like Kaji is. Also, Fuyutsuki has direct ties to SEELE and is a very old friend of Gendo's, so they probably wouldn't go after him...if only to avoid provoking Gendo too much (and causing him to lash out rather than fall in line).

Rei is neither an active threat to SEELE (so far as SEELE knows) nor expendable; she's one of three Pilots who is not also an Angel. And given just how extremely close of a call Zeruel just was, it's clear that every Pilot is needed. The Dummy Plug system was an abject failure.
 
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Fuyutsuki is...not really a practical threat to SEELE. He's just Gendo's underling-in-chief. He's not an active threat like Kaji is. Also, Fuyutsuki has direct ties to SEELE and is a very old friend of Gendo's, so they probably wouldn't go after him...if only to avoid provoking Gendo too much (and causing him to lash out rather than fall in line).
And yet it's the guy they grabbed in canon. Granted, captured instead of killed, but then, they might have just done the latter if Kaji hadn't rescued him. As it was, they accepted Kaji's death instead. Plus, in the chapter, they did say "teaching Gendo regret". It would in fact be about hitting close to Gendo, a purely punitive measure, not about removing tactical or strategic threats to them.

I mean, I still think it's Kaji because he is the asset actually spoken about, but "teach Gendo regret" would fit better to Fuyutsuki, actually.
 
"Teach Gendo regret"...hmmm...am I the only one thinking that might mean Shinji?

Think about it, they only need Eva Unit 01 for their heresy-(ahem) ritual thingy, and certainly not its Pilot. So by offing him, that means Unit 01 becomes useless and can be tucked safely away "until the time is right", whilst still having 3 operational Evangelions to deal with the remaining Angels. And as cold as he is, putting his child on life support or in an early grave is going to hurt Gendo very badly.
 
"Teach Gendo regret"...hmmm...am I the only one thinking that might mean Shinji?

Think about it, they only need Eva Unit 01 for their heresy-(ahem) ritual thingy, and certainly not its Pilot. So by offing him, that means Unit 01 becomes useless and can be tucked safely away "until the time is right", whilst still having 3 operational Evangelions to deal with the remaining Angels. And as cold as he is, putting his child on life support or in an early grave is going to hurt Gendo very badly.
Que Rei going full Proginator on everything in sight.
Between her and Kowaru, they should be able to hijack all of NERV's Evas and cause a lot of damage.
Keep in mind, neither of them have any real connection to humanity as a whole. Not enough to stop them from rampaging throughout the planet looking for SEELE. Kowaru might even have a good idea of where to look.
 
Keep in mind, neither of them have any real connection to humanity as a whole.
But both want that connection. Even when she was still (per A&T canon) drugged, Rei expressed the wish to pilot EVA so that she could have that connection to people. That's something important to her. And see her instinctive early reaction to Kaworu here in the fic. She can be instinctively protective about "her" life. And as for Kaworu, the respect for Lilim, their culture and civilization, is what has kept him from falling to the call at all, before Rei stepped in.

That being said, Kaworu alone is, as has been mentioned before, basically unstoppable, in between 1) the most ridiculous AT Field out there, 2) his ability to notice when observed and 3) his ability to command Adamite flesh. Should he ever get enraged, he is an unstoppable force of revenge. However, while he may have a faint idea about some SEELE members (Kiel?), he probably doesn't know about all of them, so "where to look" would indeed be the problem.

Of course, there is another possibility in this scenario. Rei going GNR prematurely just so as to save Shinji('s soul)...
 
"Ikari's asset." The one asset they were actually talking about is Kaji. Plus, "terminate". In canon, Fuyutsuki and Ritsuko were captured; only Kaji was killed.

Though if Kiel (I refuse other spellings) is speaking in general, it could also be Fuyutsuki, Ritsuko or Rei. Unless they somehow learned it earlier in A&T and I have forgotten that, they don't know yet what Rei is. So to them, she might simply be "Ikari's pet pilot", i.e. asset (otherwise I think they'd refer to her by her Lilith connection). Though if they are speaking about "asset" in general, then I would say the most likely bet is Fuyutsuki, because well, canon.

I feel like they'd talk about EVA-01's core in much different terms. For one, they probably know its importance to Gendo, more than just an "asset", and second they would refer to that unit with another name, seeing how central it is. Plus I'm not sure you can actually change EVA cores. The units seem to be built around them. If you could, well, then you wouldn't need to recruit the daughter of one of your chief engineers in a hurry just it was her who made the contact experiment. Then you could go about this much more planned. So I very much think EVA cores are non-exchangeable.

So my order of likelihood: Kaji, Fuyutsuki, Ritsuko/Rei.

I had my doubts that Kaji was the "asset" because they'd already been referring to him by name in their conversation; it seemed to make little dramatic sense to switch to a euphemism at the very end of the conversation. And I have my doubts that Gendo cares enough about Kaji, Fuyutsuki, or Ritsuko to really regret losing them. Granted, SEELE may not know that -- Fuyutsuki is Gendo's old college mentor, and they probably know or suspect he's sleeping with Ritsuko, both circumstances normally leading to close bonds. I'm not sure why they think Gendo cares enough about Kaji to actually regret his loss; they have no great personal bond, and professionally, Gendo would be no worse off after Kaji's death than before he started using him in the first place. An asset unused is little different than no asset at all.

One thing that does point to Kaji as the target is Kiel's mention of Gendo having "taken what was not his;" presumably they just now noticed that Adam was no longer in its safe deposit box. It's likely they figured out who's responsible.

(As an aside, just how did Kaji manage to take Adam in a way that they didn't detect? Didn't anyone check on a routine basis that Adam was still there? It's been months since Adam was stolen. Maybe he replaced Adam with a fake? Wouldn't that make an interesting paperweight when everything's over...)

I do think you're right about SEELE not knowing about Rei's connection to Lilith -- I doubt they'd be so nonchalant about her existence if they did. Without that knowledge, they may not recognize how important she is to Gendo. They have probably noted that Gendo has risked personal injury to rescue her in the past, and that Rei was the only active pilot not fired for insubordination after the Bardiel incident despite being just as guilty there. That might suggest to SEELE that he feels sentimental enough about Rei to care if he loses her. Talk about being right for the wrong reasons, in that case...

(As an aside, EVA cores were referred to as interchangeable in Rebuild, or at least removable, but that's Rebuild, not Original Canon.)

Think about it, they only need Eva Unit 01 for their heresy-(ahem) ritual thingy, and certainly not its Pilot. So by offing him, that means Unit 01 becomes useless and can be tucked safely away "until the time is right", whilst still having 3 operational Evangelions to deal with the remaining Angels. And as cold as he is, putting his child on life support or in an early grave is going to hurt Gendo very badly.

Four operational EVAs. Rei in -01, Asuka in -02, Hikari in -03, and Kaworu in -00. That said, I'm not genuinely sure Gendo would care (once Rei makes him God and reunites him with Yui, he can fix everything, right?), although, again, SEELE might assume he would.

Kowaru might even have a good idea of where to look.

I still favor Rei and Kaworu dual-synching in Unit-00 (Rei can do it because of the soul, Kaworu because it's of Adam's flesh), using the synch to share Kaworu's memory of having met the SEELE Council in person and (most importantly) experienced their AT-fields, using Rei's demonstrated AT-field-scan ability to locate each of the Council members, and use Lilith's and Adam's combined power to Tang the lot of them where they stand.

Actually, I favor that even if SEELE never manages to lay one scratch on Shinji, or anybody else Rei cares about. No need to let a problem fester if you've got a solution in hand. And eliminating the Council should remove both the SEELE deathmark on Yui and the threat of SEELE-initiated Third Impact, which should negate Yui's need to remain in Unit-01, which in turn eliminates Gendo's motivation for Third Impact.

Rei going GNR prematurely just so as to save Shinji('s soul)...

I'm not sure she'd need to go full GNR for that. NERV has the proven ability to salvage and move souls by technological means; Rei has Lilith's memory of performing a similar function in the past to seed Earth, along with some formidable AT-field manipulation abilities all her own (locating Kaworu, shaking the school, holding back Zeruel), particularly when under duress. I think this would qualify. It wouldn't surprise me if salvaging and reconstituting one human soul in immediate proximity is a simple task once she considers it.
 
And I have my doubts that Gendo cares enough about Kaji, Fuyutsuki, or Ritsuko to really regret losing them.
Of course that is true about just anyone. Short of Rei maybe, but even then only because of her quite necessary role in his plans, something SEELE doesn't know about. Still, as much as he mistreats her, he does seem to see Yui in her sometimes, leading to such outbursts as him saving her from that entry-plug. In any case, he certainly gave the most appearance of caring towards Rei. So, hm... considering just that angle, yes, Rei, is the most likely candidate.

And SEELE did talk about punishing Gendo for "taking what was not his"; not whoever actually executed the deed. So that doesn't need to be connected...

(As an aside, EVA cores were referred to as interchangeable in Rebuild, or at least removable, but that's Rebuild, not Original Canon.)
And conveniently, in Rebuild we never learn just what Asuka's deal is. And since they explicitly changed her name as a signal that we can't take assumptions for granted (not to mention her playing with her doll), it probably isn't the same story as Soryu's. Shikinami actually seems consistent to me to, well, somebody who has been subject to a harsh training program since the age of 4. Something that makes her anti-social, withdrawn, bitter and not exactly empathetic, and yet at the same time also makes her define herself entirely via that one thing she has been trained for. Anyway, the point is that my main argument for why cores in the series probably aren't interchangeable doesn't even apply to Rebuild.

I still favor Rei and Kaworu dual-synching in Unit-00 (Rei can do it because of the soul, Kaworu because it's of Adam's flesh),
I don't think that's really "synching" what Kaworu does, though. More like controlling the unit with a completely different mechanism. Rei synchs to the soul; meanwhile Kaworu directly controls the flesh. Which makes it a bit odd that Rei needs to synch with EVA-01 (and the cross synch test and her rejection by Yui before Zeruel in the series clearly show that she does in fact do regular synching), instead of controlling it the same way Kaworu did with EVA-02 in the series. Maybe it is because she only has half her soul... but notably, in the manga, it seems it is pretty much her who extracts Shinji from EVA-01 after Zeruel, and that by an ability to control Lilithian flesh. But, of course, manga. Her having only half her soul would be enough of an explanation. Or in A&T also her having been drugged - seeing as since then a whole lot of powers have returned to her, maybe that one as well...

"To hell with you, Yui. See if you can reject me now!"

Anyway, for that reason (Rei synchs, Kaworu actually just controls the flesh) I doubt your double-synch communication idea would work. However... what seems to enable synchronization is the LCL. Against Sachiel, Shinji had neither plugsuit nor, IIRC, the A10 clippings. The LCL seems to be the deciding factor. Also, during instrumentality, when all AT Fields had disappeared and souls were blurring into each other, the 'dimension' where Rei and Shinji talk is called by her the "Sea of LCL". So... if two people are submerged in LCL, especially if both are PWM like the EVAs... could they maybe synch with each other? And there certainly is enough LCL around in Terminal Dogma...

And eliminating the Council should remove both the SEELE deathmark on Yui and the threat of SEELE-initiated Third Impact, which should negate Yui's need to remain in Unit-01, which in turn eliminates Gendo's motivation for Third Impact.
Unless she wants to be an utterly immortal superbeing. Both for her own sake and because even if anything else should happen to humanity, she can still bear witness to its existence. It depends on how mentally stable she is - if we go by the manga, hooo boy. I'd go with "bugfuck insane" there. Ehem.

Of course, here she lacks the S2 organ necessary to truly be that immortal superbeing. Hm. So she might decide that she can't fulfill that aim anyway and hence, once the threats you mentioned are over, let herself be extracted...

I'm not sure she'd need to go full GNR for that. NERV has the proven ability to salvage and move souls by technological means; Rei has Lilith's memory of performing a similar function in the past to seed Earth, along with some formidable AT-field manipulation abilities all her own (locating Kaworu, shaking the school, holding back Zeruel), particularly when under duress. I think this would qualify. It wouldn't surprise me if salvaging and reconstituting one human soul in immediate proximity is a simple task once she considers it.
"New souls are only born in Rei..." Hmmm. If we interpret Ritsuko's rambling in episode 24 as that the Reis were meant as soul containers in the first place... Soul salvage by her could maybe be possible. A new body would probably require some LCL, though.
 
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I don't think that's really "synching" what Kaworu does, though. More like controlling the unit with a completely different mechanism. Rei synchs to the soul; meanwhile Kaworu directly controls the flesh. Which makes it a bit odd that Rei needs to synch with EVA-01 (and the cross synch test and her rejection by Yui before Zeruel in the series clearly show that she does in fact do regular synching), instead of controlling it the same way Kaworu did with EVA-02 in the series. Maybe it is because she only has half her soul... but notably, in the manga, it seems it is pretty much her who extracts Shinji from EVA-01 after Zeruel, and that by an ability to control Lilithian flesh. But, of course, manga. Her having only half her soul would be enough of an explanation. Or in A&T also her having been drugged - seeing as since then a whole lot of powers have returned to her, maybe that one as well...

"To hell with you, Yui. See if you can reject me now!"

Anyway, for that reason (Rei synchs, Kaworu actually just controls the flesh) I doubt your double-synch communication idea would work. However... what seems to enable synchronization is the LCL. Against Sachiel, Shinji had neither plugsuit nor, IIRC, the A10 clippings. The LCL seems to be the deciding factor. Also, during instrumentality, when all AT Fields had disappeared and souls were blurring into each other, the 'dimension' where Rei and Shinji talk is called by her the "Sea of LCL". So... if two people are submerged in LCL, especially if both are PWM like the EVAs... could they maybe synch with each other? And there certainly is enough LCL around in Terminal Dogma...

I'm pretty sure Shinji had the A10 clippings against Sachiel, but no plugsuit. Same vs Zeruel.

NERV measured an actual synch ratio between Kaworu and the EVA during testing, though, both in canon and in A&T. Presumably that means their sensors indicating nerve pulses matching up (or whatever technobabble applies) between the subject and the EVA. That suggests to me that real synchronization is going on. Another reason I think using the EVA is a good idea is that Kaworu's canon ability to set his own synch ratio to whatever he wants could enable him and Rei to use the EVA as a buffer between them, to hopefully prevent things from running out of control. Wouldn't want the plan to save the world to accidentally escalate into an Impact event, after all.

Unless she wants to be an utterly immortal superbeing. Both for her own sake and because even if anything else should happen to humanity, she can still bear witness to its existence. It depends on how mentally stable she is - if we go by the manga, hooo boy. I'd go with "bugfuck insane" there. Ehem.

Of course, here she lacks the S2 organ necessary to truly be that immortal superbeing. Hm. So she might decide that she can't fulfill that aim anyway and hence, once the threats you mentioned are over, let herself be extracted...

Shinji's conversation with Yui back in 9.17 suggested to me that she considered it a matter of necessity rather than desire:

'I'm sorry, Shinji. I had to. They knew I opposed them, and were going to erase me, like they've done for so many others. But I had the chance to be here, and I took it. I have to stop them. The whole world depends on it, the bright future I promised you.'

'Mother… what are you talking about?'

'The Angels are only the beginning. This is all part of their plan. The end of the world is coming, and nothing can stop them. All I can do is make sure I'm in the right place to derail their plan.'

Cancelling the apocalypse by cancelling those trying to bring it about would eliminate that motivation. Heck, not only would it end the immediate threat; showing it could be done could change Yui's entire worldview.

EDIT: Shinji's talked to Yui during synch... what would happen if Rei had a conversation with her, perhaps while dual-synched with Shinji?

"New souls are only born in Rei..." Hmmm. If we interpret Ritsuko's rambling in episode 24 as that the Reis were meant as soul containers in the first place... Soul salvage by her could maybe be possible. A new body would probably require some LCL, though.

She'd have LCL -- left behind by the original body after salvage, assuming she got to him before he actually died. I doubt simply reusing the same LCL would cause the mortal injury to carry over. It seems it should be possible to salvage the soul (Tanging the subject in the process, as happened in EOE, or with absorption into the EVA) and then reconstitute them on the spot, minus the injury.
 
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"Asset" could be Ritsuko, Rei, Kaji or Fuyutsuki.

If they're going after Rei, it would be because of her status as a pilot, and Gendo got a bunch of those, so they'd need to eliminate all of them to substitute with their own, which means talking about "assets" in the plural, so its not that. Besides, the pilots proved themselves to be competent fighters, so they're not going to be eliminated and substituted with inexperienced/incompetent new pilots until all the Angels are destroyed.

If they're going after Rei because of her status as a Lilith clone, that means they're denying Gendo's end game before all the Angels are destroyed, which means Gendo could lash out against them and destroy everything. If they're aware that Rei got multiple backup clones then going after her is completely pointless.

If they're going after Rei because they think Gendo cares about her, well, which is more likely, that Gendo genuinely cares about someone other than Yui or that he's faking affection to gain Rei's trust and loyalty? The same could be said about Shinji.

Kaji and Fuyutsuki are not that important to the end game and would just be a message. Because they're not important to the end game, Gendo would completely ignore said message. Whether SEELE knows that or not I don't know.

Which leaves Ritsuko. She's important enough to Gendo's plans that eliminating her would delay said plans, but not important enough to completely stop said plans and make Gendo lash out. Her control and mastery of the MAGI systems are also vital, which means hacking them would be way easier without her to help. Eliminating her would leave a opening just big enough for SEELE to exploit when they start their end game.
 
I doubt that pilots will be targeted for three big reasons:
1. Gendo have showed that he doesn't value them
2. They still need remaining angels to be killed and MP series isn't finished yet
3. Pilots aren't seen as threat.
SEELE as a whole is very risk averse so they won't be destroying assets they themselves need. So Kaji and Ritsuko are top targets seeing as they would hurt NERV without compromising their ability to fight Angels. Really valuable target is Rei tank, it's crucial safety measure for Gendo's plan with little bearing on angel killing ability while possibly pushing him into spending other Evas to safeguard Rei making him weaker at final confrontation.
 
Could they be talking about destroying Unit-01? That wouldn't necessarily kill Yui, but it would be a setback for Gendo's plans to pull her out.
 
Seriously, though, teach him regret? Gendo Ikari doing any regretting? Good luck.

Seriously, the only way Seele killing someone would matter to him would be if they somehow managed to kill Yui while she was still inside the Eva Core.
 
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