>>4078203>>4078266Firstly, Rei and Lilith are identical. Rei is Lilith incarnated as Lilin girl. There's no Lilith separate from Rei, no Rei separate from Lilith. Without Rei, the body of Lilith is hardly alive, without any will of its own, just like all the Rei clones. Whatever part of her pysche is in Eva-00 is hardly any better- just a beast of pure rage. There's only one soul, one reason, one actual human being here. And that soul is Lilith's soul, which descended to become Rei, and then returned to her rightful glory.
Now, Rei obviously has different experiences as Rei from those she previously had as Lilith, and these change her as a person. And Rei has lost her memories of being Lilith, and doesn't fully understand who she is until Kaworu more or less tells her. Nevertheless, there's still continuity at a deeper level- much like how Rei III recognized Gendou's glasses and felt what they meant to her even though she didn't consciously remember them, Rei II has feelings from her other life as Lilith- particularly her desire to protect her children that motivates her to pilot the Eva.
The question of why Rei=Lilith does what she does in Instrumentality is more easily answered when one remembers that she isn't doing it in a vacuum. She's doing it with nine S2-equipped near-gods loyal to a suicide cult assimilated to her (much like how Armisael was). She waits them out. As soon as they kill themselves as part of their rite, she goes to Shinji and settles things together with him.
There's no reason to think that Lilith's "maternal nature" compels her to return everyone to the egg any more than it compels to her to - she's a goddess, not a machine. Fuyutsuki the narrator says that it's her choice (though until Seele's Evas off themselves, I don't think it's an uncoerced choice).
