Gendo's Master Plan

[Simitus]

In You can (not) advance, Gendo Ikari is sabotaging the other NERV stations. Betany Base "accidentally" has the 3rd angel remains they were analyzing released, which eliminates Unit-05 and itself "as planned", and an explosion in America wipes out Unit-04. We don't get a good sense of other nation's Evangelion / Marduk programs except that they are limited by treaty, what is clear is Gendo views them as competition. Before the 8th angel attack, Dr. Akagi refers to Lilith and Unit 01 as top priorities. Gendo's agenda differs from SEELE's only in timetable - he wants Unit-01 awakened ASAP, regardless of the condition of the other Evas whereas SEELE's plan called for "the rest of the units" to be ready. Gendo gets what he wants after the 10th angel attack, but SEELE was ready for his treachery, scrambling Eva Mark.06 in time to stop 3rd Impact before it was complete.

In the intervening 14 years, SEELE and the world at large both turn on Gendo Ikari - SEELE for trying to steal Human Instrumentality for himself and the world nations for trying to cause a new impact. The rationale for his seemingly insane acts is doubtless that to him, they are all already dead. The entire world and human existence is just a means to an end to him. Is it to regain Yui or has his motivation become something more sinister? If it was really love of Yui he would not be sentimental towards the Rei series, and he would realize Shinji is all he has left of her. He is a man consumed. He is the perfect antagonist. And as long as he retains any of the essential machinery to produce more Evas he will keep trying. And that is why he has to die.

I'm excited to see what happens in 4. The pilots are without their machines, in the crumbling ruins of Tokyo 3 and Gendo's machinations. It is time for them to confront him, learn the truth of his lies and manipulation and save the world. And honestly I hope they do it without any more battling Evas - this is the perfect chance for resolving character arcs and hopefully Anno has gotten the existencial crisis abstraction out of his system with Shinji's rather logical breakdown in 3.

As to the Key of Nebuchadnezzar, there are a few things to read into this:

1 - the organism Kaji smuggled out of Betany base bears a striking resemblance to the brain-patterns on the deactivated SEELE monoliths, which he says could have lived forever.
2 - Nebuchadnezzar worshipped Marduk - the Marduk initiative is the name of the program that selects Eva pilots. Nebuchadnezzar also destroyed the temple of Solomon, enslaved the Hebrew race and built the Hanging Gardens of Babylon, restoring the Babylonian empire.
3 - Kaji describes it as "The guide post to unify souls unto God.", the same goal expressed by SEELE for Human Instrumentality. This further supports the idea that Gendo was trying to steal the program for his own purposes.

[Charsi]

Oh great, now you've got me looking at wikipedia.

I was thinking Gendo is more like Naboindus. Here's the wiki page for Nabonidus and here's Belshazzar's. Some excerpts that caught my eye:

Belshazzar was the son of Nabonidus, who after ruling only three years, went to the oasis of Tayma and devoted himself to the worship of the moon god Sin. He made Belshazzar co-regent in 553 BC, leaving him in charge of Babylon's defense. In 540 BC, Nabonidus returned from Tayma, hoping to defend his kingdom from the Persians who were planning to advance on Babylon. Belshazzar was positioned in the city of Babylon to hold the capital, while Nabonidus marched his troops north to meet Cyrus. On October 10, 539 BC, Nabonidus surrendered and fled from Cyrus. Two days later the Persian armies overthrew the city of Babylon.

The Book of Daniel calls Nebuchadnezzar the "father" of Belshazzar, whereas both the Nabonidus Cylinder and the Verse Account name Nabonidus as the father of Belshazzar. No known extrabiblical text indicates a blood relation between Nebuchadnezzar and Belshazzar. It has sometimes been proposed that Nebuchadnezzar was the maternal grandfather of Belshazzar; Nabonidus was a usurper and marriage to the daughter of Nebuchadnezzar might have given legitimacy to his reign. The name of Belshazzar's mother is not known so it is impossible to verify this proposal.

Nabonidus is supposed to have worshiped the moon-god Sîn beyond all the other gods, to have paid special devotion to Sîn's temple in Harran, where his mother was a priestess, and to have neglected the Babylonian primary god, Marduk. Because of the tensions that these religious reforms generated, he had to leave the capital for the desert oasis of Tayma in Arabia early in his reign, from which he only returned after many years. In the meantime, his son Belshazzar ruled from Babylon.

553 -> 539 = 14 years.

Herodotus refers to the last king of Babylon as Labynetos (Nabonidus) and claims that this was also the name of his father. Herodotus says that the mother of the younger Labynetos (Belshazzar) was the queen Nitocris whom he portrays as the dominant ruler. She is commonly thought to have been the daughter of Nebuchadnezzar.

So... what if Gendo is the Nabonidus figure (usurper of Nebuchadnezzar). Nebuchadnezzar being somewhat like Seele in this case - humanity is doing their bidding, and they have built a nice Hanging Gardens of Babylon (I mean... Toyko-3/GeoFront literally "hangs").

Nebuchadnezzar is also credited with destroying the First Temple (would that be in Antarctica by any chance?).

Interesting that Gendo happens to have stolen the key of Nebuchadnezzar from them further hinting at their identity.

How does this tie into his master plan? Well if this is anywhere near the mark, it makes Gendo is an usurper - so far so good. He married Yui to add legitimacy to his command of NERV (one of Seele's "kingdoms"). He diverges from the standard Babylonian worship of Marduk and instead worships the moon god (Lilith? here referred to here as Sin). This heretical worship allegedly put him at odds with the populace of Babylon (the events of 2.22?) and he went into retreat for over 10 years, placing his "son" Belshazzar in command.

Regarding his return, this may have had to do with the mounting threat of Cyrus and growing disagreements with Belshazzar, who was relieved of his command directly after Nabonidus had come back, along with a number of administrators.

Upon returning from retreat he immediately displaces Belshazzar and sorties to defend Babylon. He is routed and the Neo-Babylonian Empire (NERV?) falls shortly after with Belshazzar dying in it's defense.

Also note this very interesting Belshazzar story from the Book of Daniel.

From Wikipedia: In Midrash literature, after seeing "the writing on the wall" Belshazzar orders his doormen to behead anyone who attempts entrance that night in fear of his own life. But later that night Belshazzar is overcome by sickness and leaves by a back entrance. When he attempts to re-enter, he is killed by his own doormen (who smash in his skull with a heavy ornament).

Maybe Belshazzar is Kaworu, not Shinji. NERV hasn't exactly fallen yet, but with Mark.09 blown apart by Eva-02, Mark.06 beheaded and Kaworu dead, what defenses can they possibly mobilize to defend against Wunder should WILLE choose to attack?

[ElMariachi]

Maybe Belshazzar is Kaworu, not Shinji. NERV hasn't exactly fallen yet, but with Mark.09 blown apart by Eva-02, Mark.06 beheaded and Kaworu dead, what defenses can they possibly mobilize to defend against Wunder should WILLE choose to attack?

How about EVA-13 and the giant army of MP-EVAs he's building?

[Charsi]

EVA-13 is (I assume) no-go without a second pilot. Though it seems to be perfectly capable of defending itself if just one pilot is paying attention. But Kaworu is dead and I don't see Shinji getting back in it.

As for the MP Evas.. well, who knows. It would be kind of wierd if Final was a reversal of EoE, in that Misato and Ritsuko and the Bridge Bunnies et al are the attackers.

[ElMariachi]

EVA-13 is (I assume) no-go without a second pilot. Though it seems to be perfectly capable of defending itself if just one pilot is paying attention. But Kaworu is dead and I don't see Shinji getting back in it.

Gendo can always use a new Rei for the task, the problem with the soul placement is only for using the spears, not piloting.
Or he could install a Dummy System, if Kaworu isn't inside EVA-13 or is compliant enough it could work.
And truth be told we never saw what a double piloted EVA-13 is able to do in a fight, since it's only battle had Kaworu lost in thoughts and Shinji was on the defensive because he didn't wanted to harm Asuka, a shame in a sense.

As for the MP Evas.. well, who knows. It would be kind of wierd if Final was a reversal of EoE, in that Misato and Ritsuko and the Bridge Bunnies et al are the attackers.

Tat would be a fun reversal you mean?
Although I admit that the more I think about it and the more I find the 3.0 preview completely surrealist : that Gendo had some MP-EVAs is a given, we saw the transporting trains and EVA hands, but I can't see how Gendo managed to create(and especially store!) that much EVAs, unless FINAL has a big time skip, nor why he would do that : the Wunder is powerful, but not that powerful, and as awesome as Mari and Asuka are, putting such an army against them is pure overkill, even if the FankenEVA is a lie and they both have their own EVA for the fight!
Besides I can't imagine Gendo deploying such a gigantic army without WILLE noticing it, or him pressing a button to open secret doors in the ground and unleash thousands of MP-EVAs like an horde of Uruk-Haïs!

[Simitus]

@Charsi, that was some good Wikipedia digging. Playing further into religious references, the SEELE emblem is loaded top to bottom with it. The serpent encircling the apple is of course a reference to the Book of Genesis - when Lucifer deceived Eve thus imparting original sin. The Eva units being a possible word play on the matronymic "Eve", woman from Adam's rib - SEELE is deceiving the Evas. For the next element the fruit of knowledge, to which Gendo directly refers in his farewell speech to the SEELE monoliths - after partaking of the forbidden fruit Adam and Eve are cast out from the Garden of Eden, their way blocked by a flaming sword and now responsible for themselves. In his speech to SEELE, Gendo speaks lines reminscent of God's admonishment to Adam and Eve

G: "Though you have also changed the form of your souls, you are still creatures who have tasted the Fruit of Knowledge. Though you could have lived for an eternity, you cannot escape the fate of death, just like us."

Next the passage in German contained within the forbidden fruit: "Überm sternenzelt richtet Gott wie wir gerichtet". The passage means: "Above the starry firmament God judges, as we judged." It was first written in 1785 by poet Friedrich Schiller and was set to music in 1824 in Ludwig von Beethoven's 9th symphony, you better know it as 'The Ode to Joy', music frequently repeated in Evangelion but in this case most significantly as Eva-13 awakens and impact begins. Reading through the translation of the Ode to Joy after chewing on these mysteries so long is a near head-exploding experience, the text is literately loaded with meaning to Evangelion. It is almost like Anno wrote NGE exclusively drawing from this inspiration. "Seele" is German for "soul".

Next to the 7 eyes, another frequently recurring number. 7 in Revelation can alternatively be interpreted to refer to Lucifer as the 7 headed, 10 horned dragon or to the 7 spirits of God. There are 7 SEELE monoliths. As well as implementing Human Instrumentality, they seek "the killing of God that you have all abandoned." -Gendo. A goal he shares with SEELE.

That leaves only the optical illusion inverted triangle which appears at top to be isocoles but at the nadir to be 2 right triangles combined. I don't understand the significance of this element.

@ElMariachi

It seems clear a number of resources are at least still at SEELE's disposal, most significantly a series of artificial angels derived from advances in Eva technology possibly obtained as a result of the American Mark.04 project. Weaponized AT field neutralizers, more sophisticated control of Eva morphology, etc.. but I don't think all of the Eva corpses seen in Dogma or in the ruins of Tokyo-3 were ever active, at least not at the same time. There are literately thousands of them and they all appear to be discarded, ruined lifeless husks - failed experiments in the never-ending search for an Eva capable of achieving an awakened state and fulfilling the covenant of Lilith. That SEELE was guarding Unit-01's Tesseracht tells me a few things:

1 - They recognized that 01 could do what they wanted it to do
2 - They didn't trust Gendo with it anymore, or anyone once world opinion turned against them and WILLE formed
3 - They still aren't / weren't ready with enough units to bring about Instrumentality. Why more Evas need to be ready for it is in question, but it seems the Impact brought about at EOE was better planned / coordinated and had more than enough for their purposes. I would bet something like that is their plan in this version as well. 4th Impact was another attempt by Gendo, not SEELE. The precise nature of why Gendo is trying to pre-empt SEELE is the crucial question of 4.

[Stillborn]

Although I admit that the more I think about it and the more I find the 3.0 preview completely surrealist : that Gendo had some MP-EVAs is a given, we saw the transporting trains and EVA hands, but I can't see how Gendo managed to create(and especially store!) that much EVAs, unless FINAL has a big time skip, nor why he would do that : the Wunder is powerful, but not that powerful, and as awesome as Mari and Asuka are, putting such an army against them is pure overkill, even if the FankenEVA is a lie and they both have their own EVA for the fight!
Besides I can't imagine Gendo deploying such a gigantic army without WILLE noticing it, or him pressing a button to open secret doors in the ground and unleash thousands of MP-EVAs like an horde of Uruk-Haïs!

I doubt anyone could imagine 14 years time skip, rendering two movies of character development futile, Nemesis series spam as a new enemies and AAA Wunder as resistance flagship.

Honestly at this point, in 4.0 Gendo could deploy Fuyutsuki on battle field, and then make him giant with a beam from magic staff like in Power Rangers, and I wouldn't be surprised. 3.0 Opened a gate for any asspull Anno may think about.

[airman4]

Gendo can always use a new Rei for the task, the problem with the soul placement is only for using the spears, not piloting.
Or he could install a Dummy System, if Kaworu isn't inside EVA-13 or is compliant enough it could work.
And truth be told we never saw what a double piloted EVA-13 is able to do in a fight, since it's only battle had Kaworu lost in thoughts and Shinji was on the defensive because he didn't wanted to harm Asuka, a shame in a sense.


Tat would be a fun reversal you mean?
Although I admit that the more I think about it and the more I find the 3.0 preview completely surrealist : that Gendo had some MP-EVAs is a given, we saw the transporting trains and EVA hands, but I can't see how Gendo managed to create(and especially store!) that much EVAs, unless FINAL has a big time skip, nor why he would do that : the Wunder is powerful, but not that powerful, and as awesome as Mari and Asuka are, putting such an army against them is pure overkill, even if the FankenEVA is a lie and they both have their own EVA for the fight!
Besides I can't imagine Gendo deploying such a gigantic army without WILLE noticing it, or him pressing a button to open secret doors in the ground and unleash thousands of MP-EVAs like an horde of Uruk-Haïs!

Kaworu didnt said that Rei couldn't pilot because she is not a real human ?

[ElMariachi]

Kaworu didnt said that Rei couldn't pilot because she is not a real human ?

Not really : he said that the synchronized AT Field and wielding the two spears is impossible because of her "soul placement", he never specified if that implied also being unable to pilot it, though since she can perfectly pilot Mark.09, an Evangelion tied to the ADAMs, I don't see why she couldn't just pilot it.

[airman4]

Ahh i see

[gchristnsn]

Gendo intends to rewrite Seele's plan (they're trying to transform the humanity into a being with the fruit of life, to purify it from the original sin which is inherent to the fruit of wisdom, as they believe), he probably wishes to transform the humanity into a "god-like" being with two fruits and reunite with Yui in the same time.

And it's worth to notice, that in the Rebuild Marduk project assumes the creation of Wunder (the angel at the Bethany base was probably a testbed for such a craft), and Nab's key may be one of the four Adam's bodies (it actually resembles awakened translucent 01 at the end of the second movie, Kaji also refers it as a missing number, there were at least two Adam's bodies: 06 and 13, and it's unclear is 09 made from Adam's body or not).

[ElMariachi]

Gendo intends to rewrite Seele's plan (they're trying to transform the humanity into a being with the fruit of life, to purify it from the original sin which is inherent to the fruit of wisdom, as they believe), he probably wishes to transform the humanity into a "god-like" being with two fruits and reunite with Yui in the same time.

If that was the case, then their goals would be converging : both would want to make mankind evolve into a godly being with the two fruits. So Gendo must have planned something else, and its probably tied to the Key of N.

And it's worth to notice, that in the Rebuild Marduk project assumes the creation of Wunder (the angel at the Bethany base was probably a testbed for such a craft), and Nab's key may be one of the four Adam's bodies (Kaji refers it as a missing number, there were at least two Adam's bodies: 06 and 13, and it's unclear is 09 made from Adam's body or not).

Wait, from were that comes from? I don't recall the Marduk Institute being behind the researches in Bethany Base. And at absolutely no point it's even implied that marduk is behind the construction of the AAA Wunder, we don't even know from where that thing comes from.

That the experiments conducted at Bethany made possible its existence is very plausible(and that was probably the case for the nemesis Series too), but we still don't know anything about who built it.

[gchristnsn]

If that was the case, then their goals would be converging : both would want to make mankind evolve into a godly being with the two fruits. So Gendo must have planned something else, and its probably tied to the Key of N.

Nope. Seele might be a race which escaped FAR [or some opposition broken of FAR] (or even FAR themselves), which exist in the form of monoliths. They may be very religious because they act strictly in according with the scrolls (or try to make Humanity to think that they act in behalf of God, remember the slogan of Seele), and the creation of a being equivalent to "God" (FAR) is a blasphemy for them (or they would not admit this if they're FAR themselves or their representatives).
So, their goal is to purify the humanity from the "original sin", or transform it to a being with the fruit of life.
It's the one possibility remains for Gendo - a being with two fruits. Moreover, he promised some deicide to Seele and probably plans to travel to the place of FAR in a company of zillions of that green Eva-series.

Wait, from were that comes from? I don't recall the Marduk Institute being behind the researches in Bethany Base. And at absolutely no point it's even implied that marduk is behind the construction of the AAA Wunder, we don't even know from where that thing comes from.

That the experiments conducted at Bethany made possible its existence is very plausible(and that was probably the case for the nemesis Series too), but we still don't know anything about who built it.

Kaji speaks about the Marduk project at the beginning of the first movie (he destroyed the angel to setback the project). The angel there reminds Wunder and it's obvious that Wunder resides at the remnants of the base, moreover UN probably intended to use it against Nerv and Seele (so Nerv tried to slow down the project by the hands of Kaji), because Ritsuko mentions in Q that Wunder has the power sufficient to kill God.

[Shinoyami65]

Kaji speaks about the Marduk project at the beginning of the first movie (he destroyed the angel to setback the project). The angel there reminds Wunder and it's obvious that Wunder resides at the remnants of the base, moreover UN probably intended to use it against Nerv and Seele (so Nerv tried to slow down the project by the hands of Kaji), because Ritsuko mentions in Q that Wunder has power sufficient to kill God.

What?! Umm...no. Kaji didn't even appear in 1.0, he obviously didn't destroy an Angel by himself and he never mentions the Marduk Project. If you're talking about Tunniel, it was probably only released to cover his escape with Neb's Key; he doesn't mention Marduk at all in connection with it.

Gendo calls SEELE human in Q and refers to them being blessed with the Fruit of Knowledge. Gendo probably isn't planning to fulfil SEELE's mission: in Q he still continues to talk abot Yui (to the giant severed Rei head in the old command centre) and it seems that his objective to reunite with her is unchanged.

We don't know if the FAR even exist in Rebuild, and in NGE they were apparently all dead already.

[gchristnsn]

What?! Umm...no. Kaji didn't even appear in 1.0, he obviously didn't destroy an Angel by himself and he never mentions the Marduk Project. If you're talking about Tunniel, it was probably only released to cover his escape with Neb's Key; he doesn't mention Marduk at all in connection with it.

Yes, my bad, he speaks about this later: http://youtu.be/DsN5SYVphAM , it should be obvious now.

Gendo calls SEELE human in Q and refers to them being blessed with the Fruit of Knowledge. Gendo probably isn't planning to fulfil SEELE's mission: in Q he still continues to talk abot Yui (to the giant severed Rei head in the old command centre) and it seems that his objective to reunite with her is unchanged.

Yes, he wishes to reunite with Yui. But because he intends to rewrite Seele's plan, there is one possibility - a being with the both fruits. He clearly distinguishes Seele from human race.

We don't know if the FAR even exist in Rebuild, and in NGE they were apparently all dead already.

It's logically necessary, or you should accept that artificial black holes and lances are created by God.

[edit]

And there is a yet another interesting thing to add: in Space Odyssey 2001 Humanity got intelligence from monoliths, so Gendo's phrase on the gift of civilization is a yet another quote from there.

[Charsi]

Random fanwankery follows.

Although it's likely been suspected up till now I feel that likely events between 2.22 - and the events in 3.33 - represent the best evidence of a cold war / chess match going on between NERV and Seele. Both participants are making moves against one another.

An important aspect of this conflict is that both strongly desire that this little war remain quite cold and not escalate into a hot war (unlike the End of Evangelion).

The Pawns
The Project-E series (designated Eva-xx) are NERV's pawns.
The Mark series (designated Mark.xx) are Seele's pawns.

Major Pieces
Kaji is used by NERV to capture and/or remove some of Seele's high value pieces from the board.

Kaji steals the Key to Nebuchadnezzar from Bethany Base and releases the 3rd Angel. In the ensuing fight, Eva-05 (Provisional) is destroyed, but destroys the base and the Angel and brings the Marduk project to a standstill. The ultimate purpose of the Key is as yet unknown, but it can be assumed that Seele believes it is destroyed along with the base.

In retaliation Seele sabotages Evangelions 03 and 04. The activation of the latter sacrifices a neutral party base (in the US) but results in NERV having to undertake activation of the other. The outcome is better than they had hoped: one of NERV's pilots is critically injured and another quits the program after being forced to fight their fellow pilot.

Mari brings Eva-02 out of cold storage to combat Zeruel. She is ultimately unsuccessful, but her and Rei's sacrifices are crucial to convincing Shinji to pilot again.

Seele also develops and deploys Mark.06 from Taghba Base on the Moon. The existence of this "chess piece" - this apocrypha - is confirmed by Gendo and Fuyutsuki even though Seele won't let them land. Mark.06 is deployed during the attack of Zeruel, presumably to stop the Angel after it finishes mopping up NERV's remaining defenses. Shinji, however, stops Zeruel and initiates 3I. Mark.06 brings 3I to a halt with the Lance of Cassius.

The chess game drags on for 14 years, during which time a lot of bad stuff apparently happens to Earth and Shinji is told he is to blame.

Power Plays
The major pieces of this board are Kaworu and WILLE, and to a lesser extent Fuyutsuki.

Somewhere between 2.22 and 3.33 Eva-01 is parked in orbit for safekeeping. The tesseract is plastered with neo-NERV logos, so one can only assume NERV is the party responsible for this.

In addition AAA Wunder must be built or grown at some point. I theorize that Seele has the core extracted from Wunder, moving directly to stem NERV's growing power. This core becomes Mark.09. This leaves Wunder powerless, temporarily removing one of NERV's major pieces from the board.

NERV, however, carefully encourages WILLE's rebellion. They cannot overtly act against Seele so they forment the rebellion, knowing that when the organization breaks away they will take their loyal pilots (and Evangelions) with them. They also allow WILLE to take Wunder, knowing that WILLE's next step will be to retrieve a power source for their shiny new battleship.

NERV begins building Evangelion 13 in anticipation of Shinji's return. Gendo expects Shinji's retrieval (and presumably a DSS choker too). The DSS choker is quite handy for locating Shinji - it broadcasts his range after all - and Mark.09 is sent to retrieve him.

Shinji is shown a shirt (that apparently survived sitting in a shelf for 14 years without ill effects) with Touji's nametag in order to unsettle him.

Kaworu befriends Shinji, but not out of goodwill. Both Kaworu and Fuyutsuki dump additional information onto Shinji in an attempt to overwhelm and disrupt his emotional state. Their ultimate goal is to drive Shinji into piloting Evangelion 13 out of the desperate hope that he can somehow undo what he is told is all his fault: the ruination of the world. Finally, Kaworu takes his choker as a final attempt to befriend him and earn his trust.

The Checkmate

Kaworu believes that upon reaching Central Dogma he will find two lances: Cassius and Longinus. He has been betrayed and this is not the case. By this point, Shinji is distraught beyond reason and pulls the spears anyway. Mark.09 immediately beheads Mark.06 (by order) as soon as it is freed. Evangelion 13 consumes the 12th Angel that spills out and the fourth impact begins.

Until this point NERV and Seele's agents are aligned in their goals and actions. Seele, believing they've won and impact is certain, allow Gendo and Fuyutuski to turn them "off", effectively ending their lives.

The checkmate then comes in two forms: firstly, Kaworu is killed by the DSS choker. This is implied to be act of sacrifice by Kaworu himself. Seele, however, had anticipated this in the design of Evangelion 13, and the unit remains active because of Shinji's presence, keeping the Door of Guf open even as it falls from the sky.

The second comes in WILLE itself. The Wunder attacks Evangelion 13 in an attempt to stop 4I drawing fire from Mark.09. This gives Asuka a chance to defeat Mark.09 in combat, which she does, but more importantly it takes the guard away from Evangelion 13. Mari is able to jump onto the falling Evangelion's back and ejects Shinji's entry plug, closing the Door of Guf.

Door closed, impact stopped, Kaworu dead, Seele dead. Checkmate, NERV.

TL;DR: WILLE/Wunder's a pawn to draw Mark.09 away from Evangelion 13 at a crucial moment so 4I can be stopped after Seele declared victory, packed up and left.

This leaves Gendo essentially unopposed with the Key to Nebuchadnezzar still in his possession. Unfortunately, he doesn't seem to have any pilots left. It's very likely (imo) he'll be the protagonist (bad guy?) of Final.

[Rahxephon]

I got the gist that gendo, not Seele, had wanted Eva unit 03 and 04 destroyed. Gendo and Fuyutski are speaking and Fuyutski acts like he doesnt really know what happened but Gendo has his " all part of the plan " face going on, and Kaji is even spying on Fuyutski and Gendo and says Was it really an accident?

Seele wanted NERV to take unit 03 for some reason, they didnt want it destroyed, and Gendo seemed to not want it at all... unit 04 was a test bed for the s2 engine or fruit of life to solve the energy problem but Gendo wouldnt want another EVA besides 01 to become a god like being, so he probably sabotaged it somehow is what I am thinking.

I believe that just like the base where provisional unit 05 was destroyed beause of Gendo to set back SEELE's plans, the same kind of scenario happened with unit 04, and then SEELE decided to screw over Gendo by forcing him to take unit 03 when they probably knew it would become infected.

[Shinoyami65]

I got the gist that gendo, not Seele, had wanted Eva unit 03 and 04 destroyed. Gendo and Fuyutski are speaking and Fuyutski acts like he doesnt really know what happened but Gendo has his " all part of the plan " face going on, and Kaji is even spying on Fuyutski and Gendo and says Was it really an accident?

Seele wanted NERV to take unit 03 for some reason, they didnt want it destroyed, and Gendo seemed to not want it at all... unit 04 was a test bed for the s2 engine or fruit of life to solve the energy problem but Gendo wouldnt want another EVA besides 01 to become a god like being, so he probably sabotaged it somehow is what I am thinking.

I believe that just like the base where provisional unit 05 was destroyed beause of Gendo to set back SEELE's plans, the same kind of scenario happened with unit 04, and then SEELE decided to screw over Gendo by forcing him to take unit 03 when they probably knew it would become infected.

They probably didn't know it would be infected. After all, it only happened because Eva-03 happened to travel through some clouds filled with Bardiel spores as it was being airlifted to Japan.

I agree that Eva-04 was deliberately destroyed, whether by Gendo to get rid of an S^2 Engine-equipped Eva or by SEELE to produce the Mark.04.

[ElMariachi]

I get the impression that we're forgetting that in 1.0 and 2.0 there was a third player in the big chess game between Gendo's and SEELE :
- during 1.0 everything was fine : the Angels were coming, NERV was destroying them without too much collateral damages, EVA-01 was working fine and 00 was just repaired and ready for action. Gendo had his own plans but didn't acted on them yet, so for now all was fine in the world(for the bad guys).

- in 2.0, Gendo decides to begin to act to further his own agenda : his first move was to steal the Key of N, a vital component of his plan, which coincidentally is in Bethany base : if you look closely at the battle inside the base, you will see that the 3rd Angel's skull has SEELE's logo engraved on it, and even worse : the entire walls of the tunnels are literally littered by SEELE's logo! The implications are clear : Bethany base is completely under SEELE's control the same way Tabgha base is. And besides the Key, Bethany base housed two other things that bothered Gendo : the 3rd Angel whom SEELE was experimenting on(they probably wanted to learn how to control them, the Nemesis Series in 3.0 are probably a result of these research) and could create deadly weapons to use against him, and the "problematic EVA-05" as Gendo said himself... why would that cobbled up aborted thing of an Evangelion poses any problem to Gendo? Simple, the problem isn't the EVA, but the pilot : Mari is working on Bethany base, a pace under SEELE's direct command, that means that she's herself a pilot under SEELE's orders, like Kaworu. So when a definitive EVA-05 will be built and the need of a guardian for the 3rd Angel no longer needed, SEELE will be able to sent Mari to NERV in Japan to "assist" the pilots if things get sour between Gendo and SEELE(just have to freeze Unit-00 under the pretext that it's a shitty prototype compared to a Production Model and ground Rei because EVA-05 already has a pilot, and that's it!), and thus SEELE will have a direct footing on Gendo's "territory".
So Gendo made a big combo : steal the Key of N to further his plans and sabotage the base and EVA-05 so it will self-destruct, destroying the Angel, the EVA and the whole base to cover the theft of the Key and killing SEELE's own pilot. For that task, Gendo hires Kaji, a man working for SEELE but who seems to want to go to greener pastures...

- except that Kaji too has his own agenda : he and Mari are actually in cahoot, infiltrated inside SEELE and working for an hidden third party(a "proto-WILLE"). Kaji seemingly did as planed by Gendo, with the exception that he made it so Mari will be ejected from EVA-05 when it self-destruct. So everyone think Mari is dead and thus she can be deployed anywhere needed easily... which is in Tokyo-3, since that's were all the action is situated. Kaji probably helped her infiltration in the city, and at the same time is spying on Gendo.

- but SEELE discovered about Gendo's treachery, but couldn't attack him frontally : he has three EVA under his orders, Lilith as a potential hostage and there is still Angels to come. So they began their plan to little by little undermine Gendo's power and place their own pawns inside NERV :
* First by sabotaging EVA-04 so it explode and erase NERV's US branch from the map. With that Gendo lose his future EVA with infinite energy and a branch of NERV under his direct control. Fuyu and Gendo were obviously pissed off about this loss, and Fuyu and Kaji's interrogation if that was really an accident implies that someone, who isn't NERV or proto-WILLE, did it. That only left SEELE.
* Secondly, during the subsequent reunion between them and Gendo, they told him that the US government forced the Japanese one to take EVA-03 after the EVA-04 "accident", but Gendo is wary because from then on, he suspect SEELE to have discovered his plans, and thus anything coming from them is a potential poisoned gift(remember that SEELE probably command almost all of the world government like in NGE). Did the SDSS told them that it would be infected by Bardiel, or did they had another surprise stored in it for Gendo, we don't know, but the result is that in the end Gendo lost another potential EVA to use, and one of his pilots is in a coa, crippling him even more.(Shinji quitting isn't really a problem since he had the Dummy System ready)
* they reveal to him that they have a sixth Evangelion almost ready, and that they decided to use it to become a "true god" and launch the HIP, instead of EVA-01. Basically SEELE are revealing to Gendo that they have a trump card and are far from being cornered by the "unforeseen" events at Bethany base. Why did they revealed they trump card? To corner Gendo and push him to fault : Gendo will surely want to know more about this mysterious sixth Evangelion, and SEELE let him get a peek so he could confirm its existence and the fact that said EVA is almost completed. Worst, Gendo and Fuyu discovered the identity of Mark.06's pilot : Kaworu, an Angel and thus someone far more difficult to get rid from.
* Gendo has a Damocles Sword above his head, and very little time left, if he wants to still be in the race, he needs to awake EVA-01 ASAP, because SEELE is already preparing their next move : Mark.06 is finished, has a spear of Cassius with him(meaning he can one-shot any Angel at will) and SEELE is about to send him against Zeruel : the SDSS seems to have informed them that this one is extremely strong and that with its now very limited resources(Unit 00 is still under reparations and 02 frozen and without pilot, leaving only 01), NERV won't be able to scratch him. And SEELE counted on it : they probably planned to let Zeruel completely wreck NERV HQ and destroy NERV's precious Unit-01(now useless for SEELE) and then Mark.06 will intervene and kill it with the LoC, being the saviour and giving SEELE an excellent reason to impose Kaworu inside NERV as the only pilot for the only Evangelion left to fight the last two Angels!

- this scenario implies that Gendo planned to awake EVA-01 with Zeruel, because it will be impossible later with Kaworu breathing on his neck. How did he planned to do it? We don't know, maybe he wanted to use the Dummy System, maybe he asked Rei to kamikaze herself... in any case Shinji returned at the last moment to pilot EVA-01 and managed to awake it just on time, forcing Mark.06 to intervene not for killing Zeruel as initially planned, but to stopped the Third Impact that Shinji inadvertently triggered by awakening his EVA.

- the only unforeseen thing during these event is that proto-WILLE tried to interfere too : Kaji understood that if SEELE had their way, Gendo would be left as a "puppet king", and Kaji needed him and SEELE to continue their "cold war" to play them both and both brought them down. So he needed that NERV won without Mark.06 intervening. For that he used his trump card, Mari, who took control of the then pilotless EVA-02, remember that Mari was previously working in Bethany Base, officially a NERV base(even if actually working for SEELE) so her data must still be inside NERV's database, which is probably partly why she could infiltrate NERV HQ and her data available to configure EVA-02's core, letting her pilot it(Kaji must have helped her a little of course). Kaji probably hoped that between her in EVA-02 and EVA-01, it will be enough to destroy the Angel without too much damages to NERV HQ, letting Gendo keep some of his strength against SEELE... unfortunately, they didn't knew the extent of Zeruel's strength, and in the end Mari got completely owned, EVA-00 destroyed with Rei, NERV HQ ravaged and EVA-01 had to awaken to stop Zeruel, which gave an excellent reason for Mark.6 to intervene and "save the day".

The day finally ended with a stalemate between NERV and SEELE(with a slight advantage for the latter) and a complete fail for proto-WILLE.

[gchristnsn]

I get the impression that we're forgetting that in 1.0 and 2.0 there was a third player in the big chess game between Gendo's and SEELE

And the highest probability that in 1.0 and 2.0 this is UN.

So Gendo made a big combo : steal the Key of N to further his plans and sabotage the base and EVA-05 so it will self-destruct, destroying the Angel, the EVA and the whole base to cover the theft of the Key and killing SEELE's own pilot. For that task, Gendo hires Kaji, a man working for SEELE but who seems to want to go to greener pastures...

Since IPEA (Bethany may be IPEA's base [edit: or they just ruined IPEA's project there]) works for UN (fat hint is the logo), Seele gives them not so important things to research, but they're almost managed to control angels, so it was necessary to slow down them.

- except that Kaji too has his own agenda : he and Mari are actually in cahoot, infiltrated inside SEELE and working for an hidden third party(a "proto-WILLE").

Mari and Kaji are rivals (Mari spies for UN).

Kaji seemingly did as planed by Gendo, with the exception that he made it so Mari will be ejected from EVA-05 when it self-destruct. So everyone think Mari is dead and thus she can be deployed anywhere needed easily... which is in Tokyo-3, since that's were all the action is situated. Kaji probably helped her infiltration in the city, and at the same time is spying on Gendo.

Possible, Kaji may be a triple agent.

* First by sabotaging EVA-04 so it explode and erase NERV's US branch from the map. With that Gendo lose his future EVA with infinite energy and a branch of NERV under his direct control. Fuyu and Gendo were obviously pissed off about this loss, and Fuyu and Kaji's interrogation if that was really an accident implies that someone, who isn't NERV or proto-WILLE, did it. That only left SEELE.
* Secondly, during the subsequent reunion between them and Gendo, they told him that the US government forced the Japanese one to take EVA-03 after the EVA-04 "accident",

This was definitely done by Seele to retire unit 00 and replace it by 03, or less probable that it was done by UN and was used by Seele.

but Gendo is wary because from then on, he suspect SEELE to have discovered his plans, and thus anything coming from them is a potential poisoned gift(remember that SEELE probably command almost all of the world government like in NGE). Did the SDSS told them that it would be infected by Bardiel, or did they had another surprise stored in it for Gendo, we don't know, but the result is that in the end Gendo lost another potential EVA to use, and one of his pilots is in a coa, crippling him even more.(Shinji quitting isn't really a problem since he had the Dummy System ready)

Seele does not control government and hides their actions under the conspiracy (UN thinks that they protect Earth from angels).
Gendo needs 00 for his plan, so he might had poisoned 03. There was a school of pilots, but they were killed by the actual third impact then, so only Kaworu is left.

Basically SEELE are revealing to Gendo that they have a trump card and are far from being cornered by the "unforeseen" events at Bethany base. Why did they revealed they trump card? To corner Gendo and push him to fault : Gendo will surely want to know more about this mysterious sixth Evangelion, and SEELE let him get a peek so he could confirm its existence and the fact that said EVA is almost completed. Worst, Gendo and Fuyu discovered the identity of Mark.06's pilot : Kaworu, an Angel and thus someone far more difficult to get rid from.
* Gendo has a Damocles Sword above his head, and very little time left,

Possible.

And SEELE counted on it : they probably planned to let Zeruel completely wreck NERV HQ and destroy NERV's precious Unit-01(now useless for SEELE) and then Mark.06 will intervene and kill it with the LoC, being the saviour and giving SEELE an excellent reason to impose Kaworu inside NERV as the only pilot for the only Evangelion left to fight the last two Angels!

Too dangerous, they need to protect Lilith. Also, Gendo only needs to slow down Seele's plan, and would follow it until the point where he can rid off Seele. It's much more simpler when the Earth is almost uninhabited and no one would nuke you.

- this scenario implies that Gendo planned to awake EVA-01 with Zeruel, because it will be impossible later with Kaworu breathing on his neck. How did he planned to do it? We don't know, maybe he wanted to use the Dummy System, maybe he asked Rei to kamikaze herself... in any case Shinji returned at the last moment to pilot EVA-01 and managed to awake it just on time, forcing Mark.06 to intervene not for killing Zeruel as initially planned, but to stopped the Third Impact that Shinji inadvertently triggered by awakening his EVA.

He probably tried to use the dummy plug just to not to be devoured by the angel. He was very lucky that Shinji had returned (his runaway may be a result of Seele's actions, so it's also possible that they poisoned 03 to do this).

- the only unforeseen thing during these event is that proto-WILLE tried to interfere too

It's actually interesting question, why UN had interfered. Probably because of conspiracy, they thought that angel may produce an impact.