End of Eva: Why not leave from the start?

[Eliaskar]

So at the beginning of the film we see that NERV has lost their jurisdiction and legal powers and been given a warning before being hacked by 5 other Magi from around the world. Now, I can see why Gendo and Fuyutsuki would want to prevent this and they want to go through with their plan. However, why wouldn't the Bridge guy's and all the standard staff just leave? Why did they put up a fight against the government when they've basically lost their jobs and jurisdiction?

[ElMariachi]

Because they learned that barely a few minutes before said hacking and more importantly huge JSSDF assault started, it's not that NERV didn't wanted to leave, but that they didn't had the time to leave.

Beside the Japanese government was manipulated by SEELE into thinking that all of NERV was trying to start Third Impact, leading to the order for the JSSDF to kill everyone on sight, no matter if they were armed or not or if they surrendered. For the NERV staff is was a fight for survival.

Which was the perfect distraction Gendo needed to start his own version of Instrumentality with Rei. And then Rei backstabbed Gendo and everything went to hell for everyone.

[NemZ]

Better question: Wwhy didn't Gendo try and kick off instrumentality right after Kaworu's death rather than waiting around a few days for no apparent reason?

[Atropos]

According to estimates I've read, he actually launches 3I literally the day after Kaworu dies. Maybe he was just tired, or something.

[FreakyFilmFan4ever]

We see Unit 01 go through some cleansing after Kaworu's death. I'm sure any Angel DNA needed to be purged from Unit 01 so as not to contaminate Instrumentality. It could be that it needed to take a full day to be cleansed, hense the wait.

[Sachi]

Just after the hospital scene, the bridge bunnies are shown discussing their situation: they say that all access to and from headquarters has been restricted since they are on first level alert (and probably have been since the Kaworu incident the day before). Now that all the Angels had been defeated and their jobs made obsolete, the bridge bunnies had no idea what was going to happen to them or the organization so they had just been waiting for orders, and then the attack happened. Gendo likely kept them on first level alert because he was expecting Seele's retaliation.

[NemZ]

According to estimates I've read, he actually launches 3I literally the day after Kaworu dies. Maybe he was just tired, or something.

Nope. there's two full day/night cycles shown between 24 and 3I kicking off, and possible more that were simply not shown.

24 ends at night
EoE starts at the same place when it's light
Rei wakes up and in the middle of the night and leaves her apartment
Asuka's battle is in broad daylight

[Chuckman]

Better question: Wwhy didn't Gendo try and kick off instrumentality right after Kaworu's death rather than waiting around a few days for no apparent reason?

He had to fill out all the forms and get the budget requests in order before SEELE denied them and came to murder them all. There are rules, here. We're not barbarians.

[FreakyFilmFan4ever]

I still think Unit 01’s cleansing had something to do with it. You don’t want to screw up your perfect Impact because some Kaworu DNA got mixed in there somewhere, right?

[Chuckman]

Time out, we need to wash the Eva.

[Bagheera]

Better question: Wwhy didn't Gendo try and kick off instrumentality right after Kaworu's death rather than waiting around a few days for no apparent reason?

It's probably just final prep time. They had to recover Kaworu's soul, don't forget, and there were probably final adjustments that had to be made to Unit 01 before it was used for . . . whatever. A couple of days seems about right for that.

And of course, your question could be turned around: why didn't Seele attack immediately? They knew what was going on, so they could have dropped the hammer not one hour after Kaworu died. But they probably had similar issues, so.

[Ultrahuntr]

I still think Unit 01’s cleansing had something to do with it. You don’t want to screw up your perfect Impact because some Kaworu DNA got mixed in there somewhere, right?

This seems pretty reasonable to me. Especially since Eva 01 receiving the stigmata was an important part of the process.

[LordThaeon]

My bigger question would by why they don't kill Adam/Lillith after all of the other angels are dead?

Then again, Gendo probably pulled strings to keep this idea from coming up.

[Ultrahuntr]

My bigger question would by why they don't kill Adam/Lillith after all of the other angels are dead?

Then again, Gendo probably pulled strings to keep this idea from coming up.

Because that's not what Gendo nor Seele wants. If they were going to do that, they could've just done it from the beginning, could they not?

[ElMariachi]

Even if it wasn't part of their plan, they couldn't get rid of Lilith at the beginning: she's the only existing source of LCL, which is needed to create, maintain and heal Evas as well as for the pilots to synchronize with it, without it sure the Angels won't be able to trigger the Apocalypse, but they'll rather wander all around the world rampaging everything on sight, and try to stop Leliel, Arael of Zeruel without an Eva!

[The Eva Monkey]

Probably because you wouldn't expect your own government to just indiscriminately murder you without warning or provocation. Besides, how many people beyond the senior staff even knew it was coming?