My take about what could have happened between 2.0 and 3.0 :
Maybe Shinji's N3I caused the detention of all NERV personnel like we saw in the preview, and the protection of Lilith was assigned to the JSSDF, explaining all these tanks, hummers and VTOL in the ruins of the old NERV and in Lilith's chamber. To assist them : Mark.06, refitted as an autonomous unit. As for Unit-01, it stayed on confinement, still speared by Mark.06 and surrounded by Angel-sealing Hex pillars, until SEELE decides what to do with it.
If SEELE's influence is the same that it was in NGE, then they controlled in the shadows most of the worlds governments and organisations, including the IPEA and the Japanese government, and thus indirectly the JSSDF.
So by detaining all of NERV personnel for "interrogation", putting the officers of the JSSDF on charge with Mark.06, SEELE took control of NERV's HQ from Gendo, as a punishment for awakening Unit-01 while it was Mark.06 the one which was planed to become a "true god", and to make sure that he don't pull others shady schemes on their backs.
As for why Mark.06 was made into an autonomous unit? Maybe SEELE needed Kaworu somewhere else, maybe they didn't wanted to risk the life of the First Angel because the SDSS scenario said that he must stay alive; or maybe they didn't trusted him enough to let him pilot Mark.06 anymore, who knows?
Anyway soon after that, the 11th Angel appears, get dealt with, and some time after that comes the 12th. As expected the JSSDF is completely useless, and surprisingly Mark.06 too, because of the Angel peculiar body all attacks goes through him without any damage, like a stream of water. So it's decided to pull the Cassius spear from EVA-01 to use it against the Angel... which ended useless too, as the spear go through the Angel like any other attacks. The 12th then manages to reach Lilith's Chamber and shit hit the fan.
As a last ditch move, Mark.06 pulls the same move as Rei II against Armisael in NGE : it absorb the 12th Angel in its entirety, and spears itself to freeze the 12th Angel and Lilith.
Now where does Lilith's awakening and the FoIs fit in those events? My personal take : assuming that like in NGE, EVA-01 is made from Lilith and that Rei's soul is actually Lilith's, when Unit-01 absorbed Zerue's core with Rei's soul and evolved, it resulted in a completely awakened and enhanced Lilith : we have the body(EVA-01), the soul(Rei II) and the evolution brought by an ADAM based lifeform(Zeruel's core). By that logic, the resulting entity should be more or less as powerful as GNR in EoE, but was "frozen" by the Cassius spear.
When Mark.06 pulled out the Spear to try to kill the 12th Angel, Rei/Lilith's conscience awakened, and connected with the other part of her body, the one in Central Dogma, and from here I have two possible scenarios :
1/ Lilith sensed the 12th approaching the Chamber without any resistance, panicked and remotely took control of her body down there, ordering it to fight the 12th. Hence Lilith's "awakening"(which was in fact just the body being remotely commanded), her body taking the image of her soul, explaining the head changing into Rei's. A fight between Lilith's body and the 12th happened while Mar.06 was descending with the Spear. But because of the spear of Longinus in its chest, Lilith was weakened and thus losing badly against the 12th, so in a desperate move, Eva-01 used whatever magic it possesses to turn the surrounding landscape into core material, and used it to summon an army to protect the body in Central Dogma, an army created at the image of the body the soul of Lilith inhabited, hence why all the FoI are at EVA-01 image. The big problem is that with that stunt, Lilith kinda killed everyone unfortunate enough to still reside in Tokyo-3, and apparently triggered another Impact, the continuation of N3I into proper 3I...
Seeing the huge out of control shitstorm, SEELE ordered to the automated Mark.06 to spear again Lilith with the Longinus lance, absorb the 12th Angel and spear itself, the absorbed 12th and Lilith's body again to stop this madness, and to hell with the covenant with Lilith or the transforming of Mark.06 into a true god. After that, seeing how powerful EVA-01 had become, decided that the best course of action was to send this thing in orbit so that it won't create more problems and derails SEELE's scenario, they could come back for it later if they really need to.
2/ Same thing until EVA-01 got unspeared and the connection between Lilith's body down in Central Dogma and her soul in EVA-01 is made, except this time instead of remotely control it, the body get on "auto-pilot" and the 12th Angel make contact with it. Follows a "battle of wills" between the 12th Angel and Lilith body, during which all the madness around(landscape turned into core, FoI, and global death of the biosphere)happens, in short 3I for good, until Mark.06 intervene and stop everything with the Spears.
And Shinji in all of this : still trapped in stasis inside 01's core, completely unaware of the hell that was unleashed outside...
So depending on what WILLE knows, or think they knows, about everyone's roles during N3I and 3I, their resentment for Shinji could come from the fact they think that :
- had Shinji didn't pulled that little stunt against Zeruel and launched N3I, SEELE wouldn't have been able to take NERV control from them, they could have been here when the 12th showed up and would have probably managed the situation far better than the JSSDF
- maybe he was partially aware and responsible when EVA-01 awakened, hence the fear and hate they feel for that boy who tried to play with godly forces far beyond his reach.
Avatar: THE HIGHEST OF ALL HIGHS WE AAAAAAAAAARE!!!Kensuke is a military otaku who, at one point, is shown creepily taking pictures of girls to sell. He would clearly fit right in as an animator at Studio Gainax. -- Compiling_AutumnEoTV is a therapist, EoE is a drill instructor. -- ChuckmanSeriously, that is the most fananked theory I've ever heard, more than Mari being Marty McFly travelling through time to keep her parents (Asushin) together. -- Jäeger