Third Impact (Tentative Reconstructed Timeline)

[AWinters]

Anyone know how it happened??
Gendo and Fuyutsuki were observing and said that Shinji and Rei gaining a bond caused the impact - just as they planned.
Have I missed something? Because I don't understand how the third impact could be caused by an Eva, an Angel and.. learning to love.. I guess?

I also don't understand why Gendo's plan involved half the world being destroyed without human instrumentality. What could possibly be gained from that outcome?

[Reichu]

WALL OF TEXT FOLLOWS, TL;DR THIRD IMPACT IS A NIGHTMARE TO SPECULATE ABOUT

Near Third Impact

What happened at the end of the second movie was an event called "Near Third Impact", caused by Eva-01 opening the Gates of Guf to extract Eva-00's core from the interior of the 10th Angel's, merging with the 10th Angel's LCL along with the soul of Lilith inside Eva-00's core, and being restored to its two-cored "radiant giant" state from Second Impact.

Between movies, another event occurred, which was Third Impact proper. Figuring out exactly what happened requires a substantial amount of detective work -- we've been working on it since Q first came out, and we're still not 100% sure what happened. But I can fill you in on the ideas I'm currently leaning toward. Just keep in mind, the following is a tentative (at times EXTREMELY so) reconstruction, and most of it is not proven. Much of this is an exercise in very gradually trying to account for more and more details in an internally consistent way, but, given the gargantuan scale of the task, there are still some pretty big logical gaps. I'm going to phrase much of this as if it were true simply because that makes it easier to write.

Near Third Impact was deliberately planned by Gendo, Fuyutsuki, and Yui, with the intention of throwing a wrench in Seele's plans. Seele earlier in the film say that the role of the prototype will end soon, and also imply that they will use Mark.06 to facilitate the resurrection of Lilith. We see this play out when Eva-00 -- the core of which contains the soul of Lilith -- is devoured by the 10th Angel. Mark.06 departed from the Moon around when the 10th Angel attacked, and arrived shortly after the defeat of the 10th at Eva-01's hands -- the timing is rather curious, no? Seele's true intentions are further clarified by observing that Mark.06's helmet is also equipped with an empty slot for a forehead eye. This is rather interesting because, well, what happens when Eva-01 absorbs Lilith's soul? It develops a third eye in the forehead position. Ergo, Mark.06 was supposed to be the one to retrieve Eva-00's core, merge with it, and slay the Angel. Exactly how Seele could predict the Angel's behavior so accurately is unknown, but they did, and Gendo and Fuyutsuki seemed to know they could, and fortunately Yui acted accordingly. (The importance of her volition in the incident is indicated by having Gendo call out her presence in the Eva shortly before Shinji returns to Cage 7, and by Ritsuko explaining to us that Eva-01 is making the pilot's wish come true.)

So what Team YGF (Yui-Gendo-Fuyutsuki) accomplished through Near Third Impact was trapping Lilith's soul inside an awakened Evangelion, where Seele could not easily access it. At least, not without starting an Impact themselves. If Eva-01 can retrieve a soul from inside a core by such means as opening the Gates of Guf, then, feasibly, another Evangelion would be able to do the same. Finding an Eva that would be capable of doing this -- one that rivaled the power of the Eva that had defeated the most powerful Angel to date -- would be no small feat, however.

Interim

Many important events happen between Near Third Impact and Third Impact proper. Most of Nerv's personnel are detained by the Japanese government. Gendo and Fuyutsuki escape Japan and go on a mysterious adventure. Seele place Kaworu in charge of Nerv, with several Reis at his disposal. Mari is apparently compelled into cooperating -- perhaps Eva-08 is sent to Nerv from Europe under the explicit terms that it must be piloted by one of theirs (so, either Mari or Asuka). When the 11th Angel attacks, it is likely that Nerv has the standard three functioning Evas: Mark.06 piloted by Kaworu, Eva-08 piloted by Mari, and Mk.07 piloted by Rei 7. (The Vatican Treaty leaves poor Eva-02 once again frozen in IPEA custody, and never fully repaired.) Since we know that Lilith did not reach the surface during Third Impact, the blood stains on the Moon were probably left there not by Third Impact, but by the slaying of the 11th Angel. Meaning, it would have been a huge motherfucker, and it's criminal that we didn't get to see three Evas go Shadow of the Colossus on it. Blockio has suggested to me that there is imagery of a dragon and a humanoid figure hidden in the blood stains, which fits rather nicely, given the recurrent nature the "dragon" motif. (Eva-05 vs. the Third Angel channeling the tales of St. George vs. the Dragon and Marduk vs. Tiamat most obviously, but also Eva-00 wielding a shield shaped like a dragon's head against a symbolic "fire-breathing dragon" in a reference to Sleeping Beauty, and Asuka playing the role of "virgin princess sacrificed to the dragon", a la Andromeda/Cetus and Kushinada/Yamata-no-Orochi.) It's possible the 11th Angel's attack was responsible for some of the other drastic changes to the landscape that we see -- simplifies things for us if we don't have to blame EVERYTHING on Third Impact.

The detained Nerv members are freed at some point, which would go hand-in-hand with the formation of Wille. In a delightful subversion of what happened in EoE, Wille and the JSSDF join forces and make plans for a joint attack on Nerv Headquarters. In the meantime, the 12th Angel quietly attacks -- it is Ireul Redux, effectively, and goes after the Magi. The effort against the Angel ends similarly to that in episode 13, with a twist: instead of uploading an extinction program to the Angel, a program of servile compliance is uploaded instead. The Angel is brainwashed with Seele's directives, and the Magi are sacrificed to contain the transformed 12th. (Hence why they are absent from the command center in Q. Wille do not possess the original Magi, BTW: they have a copy called "Achiral".) Mark.06 is altered to no longer require Kaworu's services and run entirely off the programmed Angel* instead. The 12th is funneled into Mk.6's head through the hole for the third eye, and the hole is plugged up with a round red "cork", completely sealing the Angel within 06's restraints.

* (The cut storyboard here strangely suggests that Mark.06 actually did have an assigned pilot all the way to the end: Rei 3. Even though this might not hold true for the final film, it's still worth consideration. Notice how Rei 3's ordinal is circled, rather than crossed off, indicating she is STILL ACTIVE. Funny enough, Rei 2 is also shown as being still active, even though she was absorbed into an Angel and then into Eva-01! So the implications here are potentially quite sinister and might lend some insight into Seele's use of Reis in general.)

Day of Third Impact

On the day of Third Impact, the Wille-JSSDF joint attack on Nerv Headquarters is carried out. In parallel with EoE, this forces Seele (rather than Nerv proper) to scramble to enact their plans for Instrumentality before all of their pieces are captured off the game board. At this point, things become quite a chaotic blur and it's hard to know exactly what is going on and in precisely what order.

Seele's handling of Fourth Impact allows us to guess via reverse-engineering that, much as they "assigned" Eva-13 with the collection of Lilith's body and Mk.9 with the collection of Lilith's soul, they similarly employ a two-Eva team here. Although Mark.06 is one of the Adams, and thus the Eva in Seele's possession who would feasibly have greater ability to retrieve Lilith's soul, Seele bizarrely do not task Mark.06 with the Eva-01 problem, sending it to Central Dogma to deal with Lilith's body instead. In Lilith's chamber, Mk.06 finds Lilith Rei-shaped, enlarged, and on a different cross due to the part of Near Third Impact the second movie kept hidden from us; see this thread for further details, and it removes the Spear of Longinus from her. The Eva that is tasked with fetching Lilith's soul, then, would be by process of elimination the mysterious Mk.7. (The analogy with Mk.9 is why I previously suggested a Rei pilot.)

Mk 07 takes the Spear of Cassius out of Eva-01 since, due to Eva-01 and Lilith's mysterious link, Lilith's soul must be unbound in order for her resurrection to properly proceed. Presumably Mk.7 also has some alternative means of restraining Eva-01, and initiates some kind of procedure to extract Lilith's soul from Eva-01 at this time as well. How exactly this would work niggles me considerably, since we have little basis on which to suggest that a non-Adamsian Eva would be able to access Guf space, though perhaps, similar to Mk.9 and its blue link-forming corrosion, Mk.7 had some alternative means of drawing Lilith's soul from Eva-01.

At some point during these proceedings, Mk.6 "overlaps" (fuses) with Lilith, though the exact moment when this happens is unclear to me currently.

Similarly to EoE, Lilith awakens, drops off the cross, and starts to grow in size dramatically. She begins to phase through matter, and her head eventually begins to pass through the command center. The JSSDF do their best impersonation of Lady Eboshi and blow GNR's head off. The head is left behind in the command center, while the body 'snaps back' to Central Dogma. Things get increasingly Princess Mononoke as the headless Lilith loses her sexy Rei-like figure and bloats into an amorphous life-sucking goddess of death, with Mark.06 now establishing a giant white puppet-extension of itself where Lilith's head ought to be.

If it hasn't already started happening, the Geofront and Terminal Dogma (it's NTE, so "Terminal" is above "Central") start to reconfigure into the inverted pyramid, which extends skyward from the Black Moon on an everted Main Shaft. The JSSDF rightfully start attacking the shit out of this. Meantime, Lilith's chamber is full of VTOLs, blasting her with everything they've got.

Third Impact: A Challenger Appears!

Sometime or other, Mk.07 utterly fails to retrieve Lilith's soul and gets destroyed, and then Eva-01 is on the loose brandishing the Spear of Cassius. The JSSDF probably try to blast the shit out of her, too, as is vaguely intimated in UYCTM -- but it's Eva-01, so what the hell are they going to do to her? Since Lilith is kind of busy with her Princess Mononoke reenactment, Eva-01 might get to do the really weird stuff, like initiating the process of the Earth and Moon's coreification. And the other bits of inescapable weirdness, too, like making old Tokyo-3 collapse into the pupil of a ridiculously gigantic iris and having the ground sprout a ridiculously giant mouth. (With the iris being purple and red -- awakened Eva-01 colors -- and the teeth being red -- Eva-01 has red teeth -- Yui could have been a little more subtle about her handiwork there.)

What purpose could any of this possibly achieve? Well, in terms of the coreification of Earth, the purpose was implied back in 2.22. "Original Sin" is apparently more than a metaphor in NTE -- it's an actual curse that Seele's civilization, the Anunnaki (not official at this time, but I don't care; "Anunnaki" is so perfect I'm done settling for lame acronyms), brought upon themselves and the Lilin through their own greed and hubris. Details are currently unclear, but Original Sin is treated as a very real existential threat, a pollutant that must be removed. The purpose of coreifying Earth is to place the world and all its souls under conditions of purification -- remember the Red Earth Purification Ceremony from EoE? Yeah, a bit like that. It's also strongly channeling the Toxic Jungle from Nausicaa, complete with hordes of giant engineered beings that exist to enforce the purification conditions. So hypothetically, in the world of NTE, turning Earth is a red shithole might need to happen on a temporary basis to prevent some much greater tragedy. The question of course is who benefits from the conditions afterward? Nausicaa offers some ideas of where Anno might go with this, but I seriously need to give the manga a full re-read so I'll shut up about that.

As for the Moon and mouth stuff: remember Fourth Impact, when Eva-13 compresses a gigantic core-being into a tiny "fruit" and then eats it? The Earth was going to eat the Moon in a similar way. Compress the Moon once it turned completely to core and then OM NOM NOM. Why? The Black Moon in its current state is just an "apple core" -- it's not the complete fruit. Where's the rest of it? The Moon. (I.e., Giant Impact still happened, though it almost certainly wasn't the same thing as First Impact in NTE.) The Black Moon needs to eat the Moon to become complete again. This, bizarrely, implies that there's something special about the Black Moon's lost outer hull, but damned if I know what it is. Anyway, fully expect this to happen at some point in 3+1, what with the vague threats I mention here.

(Don't ask me why the Earth also grows a single giant mono-eye or why Terminal Dogma is secretly a transforming Eldritch location. I'm still trying to develop a galaxy-brain big enough to encompass all of this weirdness. )

MEANTIME, Lilith has taken a lot of damage, and she's starting to go Tatarigami on those JSSDF fucks. Apparently the core-grid that was created on the Moon also did a number on Lilith, and created scoring injuries over her entire body. Her skin is starting to come off, as if she's some kind of ridiculous snake person in the process of shedding, but, oh, it gets worse. The Lilith that's emerging from beneath the injured skin isn't the Lilith we know and love: it's just masses of writhing, headless white snakes. Snakes coming out of her guts, snakes popping out of her wounds, the ends of her limbs erupting into snakes one after another. Lilith is Legion -- a legion of motherfucking snakes. Those JSSDF fuckos messed with the wrong snake goddess! On Mark.06's orders, Lilith starts to liberate souls from their bodies. Everybody who's anywhere near any part of Lilith is screwed. Seele have her doing this so that she can send everybody back up into the skywomb, because they're Seele and where else would they send everybody?

Third Impact: Failure x Infinity

But, oh, Seele's loyal little Angel pet inside Mark.06 has to contend with the fact that Mk.7 never delivered Lilith's soul like it was supposed to, so now it's got those Ayanami jerks (and maybe Shinji too, but he doesn't remember anything so who cares about him) wagging their fingers, going, "I'm afraid I can't let you do that, Ireul-kun." Team YGF (or maybe just Team YG; I don't even know anymore) has something else in mind for everybody's souls. So this is how we end up with the Failures of Infinity. Lilith isn't able to collect anyone properly to send into the Gates; they get turned into weird Eva-01-looking things instead. The souls that are at the epicenter of the Impact are brought in contact with Lilith's LCL and are placed within effectively perfect, however headless, copies of Eva-01 -- compare to how a perfect giant Rei was formed from the remains of the 10th Angel. The poor shitheads who got swallowed up into the coreified Earth's crust, on the other hand? That's core, not LCL -- they get a shittier deal. Remember Eva-01 trying to extract Rei through the 10th Angel's core, and all those deformed little Rei effigies started forming instead? Similar principle here. The force pulling on the souls that lie outside the Impact epicenter is not sufficient to extract them from the mega-core, and so tons of deformed little Evas start to form instead. These poor souls apparently know what a raw deal they got, because they immediately start to combine with each other, as if trying to smooth out their flaws. (Hello there, visual metaphor for old-school Instrumentality!) By the looks of things when Third Impact got frozen, it wasn't working all that well. Brownie points for trying, though.

So anyway. Once Eva-01 is satisfied that she's thoroughly ruined Seele's (and a whole fucking lot of other people's) day, she decides that she's had enough fun. Time for some sweet, sweet revenge. She takes that Spear of Cassius and goes down the Main Shaft, where the Eva-headed snake monster is. She takes aim! She throws! It's like the end of 2.0, just with the roles reversed! What gleeful satisfaction as the spear goes straight through that Mark.06 bitch! Hah, look at her squirm and try to pull it out! ...Wait, pull it out? Tsk tsk, that simply won't do. Sighing, Eva-01 descends the rest of the way, her dramatic moment of triumph forever ruined. She fetches Longinus from wherever Mark.06 had tossed it, and drives that sucker into Lilith's back, all the way through. Good -- this time, the snakes stop writhing and Lilith goes still. Very good. (This is what kills Lilith? I guess? Somehow, maybe?? Very unclear.) Eva-01 goes to sleep shortly after that.


I completely neglected to account for the big plug of FoIs in the shaft that looks like it got sliced through with someone's halo, along with all those fleshless bleached-white skulls just piled in Lilith's chamber (which somehow belong to the FoIs even though they aren't Eva skulls and don't seem to have ever been attached to the FoIs), but, hey, just be glad this account of 3I made THIS much sense. Hard to believe all that nonsense above is the product of years of galaxy-brained thinking. Anno is an evil, wonderful man. Well, someday we'll be able to put together a mostly coherent sequence of events. ...Someday.

[AWinters]

Thank you for catching me up on the current theories. That's a lot to absorb. I thought the rebuild was toning down the obscure puzzles, but it sounds equally (if not more) complex!

[Reichu]

Thank you for catching me up on the current theories. That's a lot to absorb. I thought the rebuild was toning down the obscure puzzles, but it sounds equally (if not more) complex!

Yeah, it definitely is a lot to absorb. Even after all these years of becoming intimately familiar with everything, Q is still an amazingly hard nut to crack, as you can see from the places where my attempted timeline doesn't quite work. There's so much going on and so much to take account of that -- pending the possibility that Shin will clarify enough of it to make it finally possible to solve in a more straightforward manner -- one basically has to juggle at least a dozen "what the hell is going on and why?" threads concurrently. Lots of progress has been made, but there is such a long way to go. If you need further clarity on any specific item, don't hesitate to ask -- the right questions could help me figure out some of the areas where I'm still struggling, honestly!

Ohtsuki from King Records made a lot of strange claims on Anno's behalf toward the beginning of production, and these statements were widely spread through early "Rebuild" publicity and really helped set the tone for how the movies were received. This whole idea that they are "lighter, softer, and simpler", only for Q to come out and flush that whole idea down the toilet completely. Q's level of information density is really amazing -- it has to be both itself AND the movie that was skipped over. Crazy.

[AWinters]

Yeah, I have been bombarding the forums with questions lately Sorry it's a bit much.
Started rewatching them all in one go after so many years and it hit me that I don't understand half of what's going on.
It became evident that all of Evangelion is one big complicated puzzle with missing pieces and all we can do is theorise what the missing pieces look like and hope we put the rest of it together correctly.

Yourself and this forum are helping greatly. I initially tried the Facebook groups, but turns out they know even less than I do (which isn't much).
Now I only give them my "just had an amusing thought" kind of not serious questions and save the genuine questions and thoughts for here.

[Dr. Evangelion 047]

That's an interesting timeline, Reichu. It differs from what I thought I had gleaned from the Rebuild's bits and pieces, and I think fails to account for some details.

So, here's my take. It's not as deep, but I've tried to assemble it based only on what we were shown. I assembled this a long while ago in response to a lot of people saying that N3I and Third Impact 'didn't make sense.'

• Near-Third Impact takes place. Tokyo-3 is destroyed. Kaworu stabs Unit 01 with the Spear of Cassius.
• Unit 01 is trapped inside those anti-Angel pillars, still impaled on the spear.
• Quickly, the UN takes control of NERV. Either through bureaucracy, or EOE-style direct action. The logo is changed/rebranded. The change of the logo is important, as I think it reflects the state of NERV post N3I - it's all digitized, perhaps handed over to the MAGI entirely. Reflecting this, Mark 6 is turned into an autonomous unit. People don't want kids piloting the god-machines anymore! Angel 11 attacks but is stopped by neo-NERV.
• Angel 12 attacks and manages to make its way to Lillith's chamber. Third Impact kicks off. Mark 6 descends, beheads Lillith, takes Angel 12 into itself and impales itself with the two spears. The UN forces are either lost there defending Lillith from the angel, or attacking her. Third Impact is cut short.
• Unfortunately, the world is still devastated. You get Teeth Canyon, Crazy Close Moon, whatever. Following this, that seal is placed over Lillith's chamber because no one knows what the fuck to do about it. NERV is basically dead at this point.
• Gendo and Fuyutsuki, who escaped the takeover of NERV by hiding in the mountains, resume operations in NERV HQ. For the most part, the world lets them be because they have better things to worry about than two old men playing house. Kaworu returns, too, and SEELE also move in. Kaworu becomes Gendo's 'jailer' to prevent any more shenanigans. Due to the sheer level of automation invested in NERV, they are able to actually get things semi-workable again.
• Time passes. Unit 02 is patched up. Various EVAs are built.

Here are the things that were unclear to me.

• When was Unit 01 shot into space? It features the new NERV logo, so, going by this theory it was after the rebranding of NERV. So, this means it might''ve taken place before Third Impact proper. However, this would mean Shinji's role in Third Impact - if at all - is impossible. I feel it's less likely that it was shot into space after Third Impact, given the state of the world, but it's also possible. Either way, it's unlikely that Gendo would've parted with it, I think.
• How did Lillith's head end up in Central Dogma? Given that the giant red Evas are reaching for it, it seems to have happened before they were created. On the other hand, given that Lillith's body seems to be either melting or reconstituting itself, maybe that was where Mark 06 decapitated her and then descended down to Terminal Dogma to finish the job?
• The spears - what happened to them? I doubt Gendo could get past the barrier and swap them out. Did Kaworu just not know that the Cassius would alter shape after being used?
• When was WILLE formed? I assume it's after Gendo and co. kick NERV online again, given that they seem to be something of a clandestine anti-NERV organization.
• When did SEELE move into NERV HQ? Why?
• Is the Wunder Pen-Pen?

Another small thing is that Unit 01 is referred to as the 'trigger' of Third Impact. So, someone 'pulled' the Eva to kick off Third Impact. If people thought Shinji was inside, then there's no wonder people assume he played a part in it. Unit 01 is also called a 'catalyst' and not an instigator or initiator. So, Unit 01 was something that make Third Impact happen more quickly.

[Reichu]

"I tried to assemble mine based only on what we were shown" -- I don't want to assume anything here, but this could come off as rather ... uncharitable toward the other party, no? I wouldn't expect my reasoning to be obvious in a quick and dirty overview, and I'm happy to elaborate on how I arrived at any given train of thought -- no assumptions necessary.

Also, out of curiosity, what do you think I'm failing to account for? (Not to imply I'm in any way accounting for everything.) I am always looking for ways to hone my own mental framework, and I do see some things you mention that I glossed over in the write-up (some omissions were inevitable, really), but you also mention being niggled by points that I discuss quite specifically, like Lilith's head.

The thing about a "catalyst" sounds like the old github translation. I might have been responsible for that word choice myself and I regret it quite a fair amount. What Kaworu says is closer to "root cause". In which case, any issues here are accounted for by remembering that Lilith's soul is inside Eva-01 and that this makes Eva-01 "part of Lilith". Q implies some rather bizarre "quantum magick" shenanigans with Lilith's body and soul -- like how the body and head remain metaphysically linked, and how Rei 6's soul is "somewhere else", i.e. inside Eva-01 proper -- and taken to its logical conclusion, it means that Gendo is communicating with Yui via the Eva-01/Lilith link (remember him talking to the head?). In terms of 3rd Impact, the link means that, as I noted, Seele would not be able to resurrect Lilith without first removing the Cassius from Eva-01. This would result in Lilith's body being reawakened (see: previous link to thread about Lilith's off-screen re-crucifixion) in turn.

I used to think that Mk.06 did not start off 3I being infected with the Angel, but the visual association between the 12th Angel and Ireul along with the fact that the Magi are simply NOT THERE in Q got me thinking about the matter a bit differently. The fact that 6's armor is capable of holding the Angel completely inside and the Eva must be forcibly cut open to release the 12th also shows that the infection was done on purpose under controlled conditions. Take note of the plug in the 3rd eye hole especially (which I mention in my write-up) -- this was not there in 2.0 and creates a complete seal. This isn't every reason but it's enough to get one seriously questioning.

[AWinters]

Is there an explanation as to why the gate of guf needed to be open to rescue Rei?
The only conclusion I've been able to come to is that the inside of the Angel's core must be on another dimensional plane. Otherwise, he should have been able to use physical means to get her out.

I'm also struggling with what gave Unit 01 the capability to generate a halo that would become the gate.
I expect that there's a "formula" for creating an impact, which I'd assume the spears were a main part of if it wasn't for this scene.

Sorry if I missed anything obvious in your response. It's taken me a long time to break it down and absorb what I can.

[Blockio]

Is there an explanation as to why the gate of guf needed to be open to rescue Rei?
The only conclusion I've been able to come to is that the inside of the Angel's core must be on another dimensional plane. Otherwise, he should have been able to use physical means to get her out.

I don't think that opening the gate of guf was a necessity, but simply a side effect from the forces at play when Unit 01 awakened. Shinji pretty obviously didn't know the scale of events he was causing, so I doubt that he consciously oepened them.

I'm also struggling with what gave Unit 01 the capability to generate a halo that would become the gate.
I expect that there's a "formula" for creating an impact, which I'd assume the spears were a main part of if it wasn't for this scene.

To create an impact event in NTE, you have to involve one of the four Adams, so either 01, 06, 13 or the key of Nebby. The spears are just there to control the specifics of how the impact will unfold, not directly related to causing them; that's why despite Kaworu saying that these were "not our spears", the impact event still took place; the difference is simply in how the fusion of souls would have looked

[AWinters]

Thank you for the help.

I don't think that opening the gate of guf was a necessity, but simply a side effect from the forces at play when Unit 01 awakened. Shinji pretty obviously didn't know the scale of events he was causing, so I doubt that he consciously oepened them.

I figured that the gates were opened by either Yui or the beast. Shinji couldn't see anything that was going on from inside of what I can only assume was an interdimentional breach.

[Kendrix]

Just from the fact that the FoI are EVA-01 shaped, EVA 01 must have been involved.

If it wasn't that would be a total copout & all the emotional arc of Q would be null & void.

Perhaps it was sealed on the surface for a while (as in the trailer) until it eventually reactivated - as a response to whatever shenanigans were going on with Lillith and the interim Reis, because a piece of her soul ( the one that became Rei II) was in EVA 01.
It must gave gone to space relatively late - As per the NEO Nerv logo on it, and a Nemesis series/Mark Four packed in with it - quite possibly after actual TI.

Maybe it was something like they nearly averted an EoE style impact but it failed/ there was still mass devastation because of EVA 01 somehow.

[StrokeMeGoat]

[quote="Reichu#896726#896726"] (This is what kills Lilith? I guess? Somehow, maybe?? Very unclear.) /quote]
I think Mk.06 being referred to as the True Evangelion and wearing Lilith's mask from NGE during its development is a clue that Lilith's DNA was "plunged" into Mk.06 using a Spear of Longinus a la the NGE Adam Contact Experiment. Either this didn't result in pseudoevolution into a Radiant Giant and the opening of the GoG because prior to being outfitted with the autonomous Angel pilot the Mk.06 lacked an S2 engine (Kaworu could activate the unit without one), or Kaworu himself as the First Angelis somehow able to prevent the GoG from opening and/or keep Mk.06 from awakening. At this point, Mk.06 has undergone the appropriate transformations to become an Adam-Lilith necessary to serve as a surrogate body for Lilith to merge with so that she can assimilate with the other Giants of Light to become a whole, perfect, unified being.

But, the bastardized union of Mk.06 and Lilith that actually occurred as the result of Unit-01's awakening and Near Third Impact only took place the way that it did to serve as an insurance policy for SEELE. The idea is that the merging of the Angel, Mk.06, and Lilith would result in an impact that they could postpone indefinitely as needed using the Spears, which prevents team YGF from using Lilith in some manner other than they desire or even outright killing/destroying her to circumvent the fate of experiencing the Impact and permanently disabling SEELE from carrying out their covenant with Lilith. Mk.06 wasn't supposed merge into Lilith, Lilith was supposed to merge into Mk.06. The result is that upon merging and as the opening rites of the Impact began, Lilith's body lost all possibility of ever sustaining itself separately as a unique entity distinct from Mk.06.

Assuming you're correct about how things transpired with Unit-01 replacing the Spear of Cassius with Longinus, then I think the reason two spears were required to totally immobilize the Mk.06-Lilith is because the Mk.06 itself possessed both Lilith's DNA and therefore probably the FoK as well as its own S2 engine in addition to the Angel with its own FoL/S2 Engine. While decapitating Mk.06 is necessary for releasing the 12th Angel, I don't think that necessarily means that the Angel had to be contained in the head. The basalt looking metal snake entity emerged from both ends of the neck, not just the end attached to the head. Besides, from what we know, beings composed of Particle-Wave Matter should just homogenously merge with the physical form of whatever being they become one with. The spear Mk.06 is trying to pull out is penetrating its core, meaning its incapacitating the S2 engine of whichever being is contained within it (it could work regardless of whether it is the 12th Angel's or its Mk.06's),and the other spear is penetrating more specifically the merged body. As far as we know, a single Spear is only capable of incapacitating a single SoL/Giant of Light or more specifically its soul. With both an Angel and an Eva with an FoL, two spears were needed, and one had to penetrate the core.

It's also a distinct possibility that Kaworu's soul was placed within Mk.06 and that's actually potentially even integral to the control system for the autonomous Angel Pilot mechanism. Assuming the angel is like Iruel and assuming the Magi are capable of reprogramming the Angel on their own may not even be required if Kaworu's soul, as the First Angel, is able to dominate the souls if its children and effectively produce compliance that way. Kaworu claims that two souls are required to be synchronized in harmony to overcome the barrier to Dogma, but since when do we trust the word of somebody as duplicitous, manipulative, and creepy as Kaworu has shown himself to be in NTE? This would allow me to avoid my workaround of saying that there need to be two Spears to incapacitate the Mk.06-Lilith because the Angel and Eva both possess FoL, because then there are actually two souls present, and it also goes a ways to explaining how Shinji was capable of totally rejecting Kaworu's will and overriding the controls for Unit-13. I mean, didn't it always seem a little strange that somebody so distraught and disturbed with the situation they were in upon noticing the Spears were both the same, and so adamant when pleading with Shinji not to go through with removing the Spears wouldn't intervene? Shinji himself even remarked that Kaworu wasn't helping with Asuka anf Mari. Perhaps it wasn't just that Kaworu was totally preoccupied, but rather that his being so preoccupied meant the fact Shinji was piloting the Eva on his own was no longer something he was covering up by pretending to be doing things "in synch" with Shinji?