There is something I always tough odd during the fight between Asuka and Shinji : why Kaworu never tried to help Shinji in trying to reason Asuka?
I understand that he was deep in thoughts because he felt something was wrong... but right in front of him there was a German fury hellbent on skewering them with a giant glaive, and his partner had all the difficulties on the world to keep her at bay because he didn't wanted to harm her, and they magical drones were being destroyed one behind the other!
Basically during that battle Shinji wanted to make understand to Asuka that he didn't wanted to destroy the world with the spears, but to actually save it, and her answers where interesting :
Firstly when Shinji tells her that he's indeed piloting and that will change the world by doing it, she responds :
01:09:15 {Asuka} If that's how it is, don't pilot!
Secondly, when Asuka asks if Shinji wants to cause 3I again, Shinji responds that no, he don't want to finish the world, but to save it with the spears, then Asuka leans back, scowls at him and deliver that line :
01:10:16 {Asuka} You really *are* a little brat.
The way these two lines are said, it looks like Asuka don't see Shinji as an enemy, but as someone who said something really wrong and/or stupid, and can't believe he actually said that. It looks like Asuka knows, or think she knows what will happen if Shinji pull out the spears.
Now let's going back in time, when Kaworu explained his plan to Shinji in his room :
01:02:34 {Kaworu} Ikari Shinji-kun, your only hope lies with the two Spears left at the Impact epicenter in Dogma.
01:02:41 {Kaworu} They are the keys to invoking the Instrumentality Project.
01:02:45 {Kaworu} We should take those Spears for ourselves.
01:02:48 {Kaworu} That way, Nerv can no longer trigger the Fourth Impact,
01:02:52 {Kaworu} And if we use them together with Eva-13, we can even repair the world.
By NERV, Kaworu was probably designing SEELE, as he though that Gendo, and thus neo-NERV, came back to following SEELE's scenario, if not he wouldn't have been so much surprised by Gendo's little trick with the spears. Anyway, what's important is that apparently the two spears a essential to trigger Instrumentality.
Now back to WILLE and the fight in Lilith's chamber : WILLE seems to have learned a lot of things about SEELE's plans, and indeed when the DSS Choker detected a unknown until then pattern blue(Kaworu's), she looked
very surprised :
01:16:13 {Mari} Blood type blue from the DSS Choker?
01:16:15 {Mari} But there shouldn't *be* a Thirteenth!
The number and order of apparition of the Angel are consigned in the Secret Dead Sea Scrolls. The fact that Mari, a member of WILLE, know at least that there should be only twelve Angel is a sign that she must know about the SDSS, indeed if someone wants to fight SEELE knowing about these scrolls is of vital importance since all of SEELE's scenario is based on them.
Added to Asuka's behavior toward Shinji, that could imply that WILLE knows how SEELE wants to launch Instrumentality, by using the two spears.
So the logical conclusion is that Asuka and Mari didn't saw Shinji as an enemy willingly working for neo-NERV and SEELE, but as a "neutral party" being manipulated by the bad guys, who made him think that he can be an hero and save the world if he retrieve the two magical spears.
Except that Shinji already knows what NERV intends to do with the spears, and he's actually trying with Kaworu to double-cross them... so then, why did Kaworu said nothing? Why didn't he at least tried to corroborate Shinji's claims that they aren't trying to finish 3I's job? The guy is obsessed by Shinji, he must be one of the people who knows the most how Shinji works, even if he was deep in thoughts, he should have seen how much having to defend against Asuka was putting him dangerously close to the edge, and should have at least tried something to defuse the situation before it ends up completely out of control.
Instead of that, he kept talking only to Shinji via the internal communication system, as if he absolutely wanted to make Shinji stop without having to interact with anyone else.
Now let's come back again, when Kaworu explained to Shinji what happened to the world :
00:50:55 {Kaworu} Mass extinctions are not unusual on this planet.
00:50:58 {Kaworu} In fact, they help drive evolution.
00:51:02 {Kaworu} Life has always changed itself to adapt to the world around it.
00:51:08 {Kaworu} However, Lilin change not themselves, but the world.
00:51:15 {Kaworu} So they brought the rite of artificial evolution unto themselves.
00:51:21 {Kaworu} Old life is offered in sacrifice,
00:51:23 {Kaworu} so that new beings blessed with the Fruit of Life may be created.
00:51:29 {Kaworu} All this is an act of extinction that has been programmed since time immemorial.
00:51:33 {Kaworu} Nerv call it the Human Instrumentality Project.
And back to his conversation in Shinji's room :
01:02:34 {Kaworu} Ikari Shinji-kun, your only hope lies with the two Spears left at the Impact epicenter in Dogma.
01:02:41 {Kaworu} They are the keys to invoking the Instrumentality Project.
01:02:45 {Kaworu} We should take those Spears for ourselves.
01:02:48 {Kaworu} That way, Nerv can no longer trigger the Fourth Impact,
01:02:52 {Kaworu} And if we use them together with Eva-13, we can even repair the world.
Kaworu actually never, ever mentions SEELE to Shinji, not once. Why? Saying to Shinji that Gendo is working for a secret organization wouldn't have changed Shinji's resolve to stop his father. Instead of that, by always citing NERV when talking about is trying to bring Instrumentality and who Kaworu is trying to thwart by keeping the spears for themselves, and since by that point NERV = Gendo(and Fuyutsuki), Kaworu is turning Shinji against Gendo, but
not SEELE, as Shinji didn't even know they exist.
In NGE, Kaworu's reason to betray SEELE was that after learning more about the Lilin, he fell in love with them, their culture, their achievements, and thought that SEELE was in the wrong path in trying to erase all of this under the unification of Instrumentality. In the manga, his betrayal comes from his will to chose his death, his "only freedom", on his own terms, so basically out of spite against SEELE, and besides he told Shinji that even if he makes contact with Lilith, the Third Impact that would follow wouldn't annihilate mankind, but make it evolve into something else.
But here in Rebuild, what are Kaworu's motivation? Shinji's happiness. Why is he betraying SEELE? For Shinji's happiness... but is he really betraying SEELE, after all we only saw him talking about thwarting NERV(=Gendo)'s plans, he never talks about SEELE.
And when he talked about the "rite of artificial evolution" that the Lilin brought into themselves, he said that it "has been programmed since time immemorial", like it was mankind's destiny. But not once did he said that SEELE's "rite of artificial evolution"(i.e. Instrumentality) was wrong, unlike in NGE, he only talked about NERV.
So here goes my theory :
what if Kaworu actually stayed loyal to SEELE to the end? What if Kaworu was working to bring forth SEELE's Instrumentality?If Kaworu though that Instrumentality indeed was mankind's destiny, and that all that SEELE wanted this time was the "peaceful purification of all souls" brought by Human Instrumentality, why would SEELE's goal be incompatible with Kaworu's objective to make Shinji happy? After all we don't know what he meant by "making Shinji happy", and he was talking about that even before 3.0 where making him happy would simply be letting him fix the world. So what if Kaworu's goal was to make Shinji the center of Instrumentality so that he could temporarily become a god and shape a world to fit to his own definition of happiness. Shinji would create his own happiness, SEELE would have their purification of the soul they wanted so much, and everyone is contented!
Sounds crazy? Well remember that Yui had a similar plan for Shinji in NGE and the manga : putting him at the center of Instrumentality, so that he would be the one to decide if mankind should be saved and given the choice to return to reality, or if mankind should be shaped into something else to erase the pain brought by their existence. And Yui had only Shinji's best interests at heart(at least what was his best interests in her head), so why wouldn't Kaworu, someone literally obsessed with making Shinji happy, have a similar plan?
Last thing, you must all have noticed how SEELE didn't really gave a shit that Gendo betrayed them and turned them off, implying that he also had something planned to get rid from Kaworu, and their response?
01:17:21 {Seele 01} Our wishes have come to fruition.
01:17:25 {Seele 01} Good.
01:17:26 {Seele 01} All is well now.
01:17:29 {Seele 01} We wish for Human Instrumentality, the peaceful purification of all souls.
By the look of it, they already got what they wanted. You could think that it was Mark.09 about to hijack the Wunder... but frankly, how could the Wunder fit into SEELE's plan to trigger Instrumentality? Maybe they wanted to capture it to have a emergency plan by retrieving EVA-01, but betting everything on the chance that one EVA will be able to hijack a flying fortress protected by other EVAs seems a little flimsy for a bunch of guys who planned Instrumentality for thousands of years, so what could they have been talking about that basically told to Gendo "suck it, we still win little boy!"?...
01:25:41 {Kaworu} We'll meet again, Shinji-kun.
Yep, their "boy" as Gendo calls it is still in the run, and will probably act during Final, as he made it clear to Shinji that they
will meet again!
So ladies and gentlemen, mark my words, SEELE isn't done yet, and we will still hear of them in FINAL!
On a side note, if my(somewhat crazy) theory is true, that would have the benefit to shed a new light on WILLE's actions at the end of 3.0 : that would mean that no matter how were the spears, if there where two different like Kaworu and SEELE hoped, or two of the same type like Gendo planned, WILLE were doing a good thing, preventing any kind of Impact or Instrumentality since in any cases an Impact and/or Instrumentality would have happened, and that indeed Shinji was completely manipulated since the beginning!