Ah! It’s fine if you haven’t read my essays (that tag is truly daunting, I know). And no, I haven’t answered this yet! I’m still on mobile, so I apologise for the lack of images and if autocorrect fudges anything gup (writing all of this out is pretty taxing on the thumbs, phew).
The simple answer: the soul residing within Unit 00 is the other part of Rei/Lilith’s soul.
To be honest, I wasn’t aware that anyone thought that Unit 00’s soul was Naoko, or that there was a controversy at all. Oops. I should read more analyses of Evangelion by other people, I guess. I can understand why one could come to that conclusion, though, since Naoko is indeed a “mother” (like Yui and Kyouko, the souls of Unit 01 and 02 and the mothers of Shinji and Asuka, respectively) and since Naoko would indeed hold a grudge against Ritsuko, Rei II, and Gendo (considering the two times that Unit 00 went berserk during testing).
However, it’s pretty painfully clear that the Unit 00 soul is the other part of Rei. When Gendo created a genetic clone of Yui, he required a soul for the clone to live; he extracted Lilith’s soul (similar to how SEELE extracted Adam’s soul to place into Tabris/Nagisa Kaworu). Rei I was a cruel child who smirked viciously whilst cutting Naoko down in the most brutal manner possible. It’s possible that Rei may have simply been repeating what Gendo had said, but the cruel smirk on the child’s face hints otherwise. After Naoko’s murder of Rei I and suicide of herself, Gendo split the soul in two. The motherly and vicious qualities went into the EVA; the rest went into Rei II.
The origins of Rei II’s lack of emotional response and complete apathy hold multiple possible roots. I hold that Rei has schizoid personality disorder, or at least symptoms very akin to SPD. It’s possibly that Rei’s childhood, trained to simply be a submissive soldier and never seen as a person except as a replacement for Ikari Yui, caused the First Children to develop said apathy. It’s possible that the medicine that Ritsuko gives the First Children (as seen in Rei’s apartment) serve, either primarily or additionally, as suppressants, in order for Ritsuko and Gendo to work with the most docile, obedient pilot possible. It’s possible that only having part of the soul left Rei without the necessary components to fully experience emotion (we do know that splitting the soul can result in insanity and the desire for death, as seen in Asuka’s mother). It’s most probable that the First Children’s apathy/SPD-like symptoms arise from some combination of the above and other potential causes.
Rei I, particularly the more vicious part, would definitely bear a grudge against Gendo, against Ritsuko (as a stand-in for Naoko, in the Evangelion theme of the child becoming the parent), and again Rei II, the part of the soul that is “free” in some sense. Unit 00’s berserk moments certainly hold in that manner.
Even more telling: During test in which Shinji and Rei switch places, Shinji momentarily connects with Rei/Lilith in Unit 00, identifying the presence as Rei, after which Unit 00 goes berserk. When Rei enters the plug of Unit 01, the First Children comments that the plug merely smells like “Ikari-kun”. By contrast, Shinji has a distinct impression of “Ayanami”, to a point of seeing flashes and so forth. Which, again, is followed immediately by Unit 00 manifesting agency and going berserk. As well, in episode twenty-three, when Armisael infects Unit 00, Rei II attempts to identify the presence, first as Rei II, then as “the me in the EVA”, and finally as the angel. “The me in the EVA”, which is distinct from both Rei II and from Armisael? Seems like the only logical explanation is the Rei/Lilith soul-part in Unit 00.
Following Rei II’s self-sacrifice in that twenty-third episode, the First Children seems to become colder again. Quite a few people consider this backwards character development. But not at all: because Unit 00 was also destroyed, Rei III now contains the full Lilith soul, the same soul as was in Rei I. Rei III recalls the years spent in the EVA, understands emotion better than Rei II, and recognises Gendo as the piece of shit that he is. Rei III also either is aware or becomes aware that the soul within the body is Lilith. Rei III, if you recall, dislikes Gendo, as visible in the First Children’s interactions with Gendo’s glasses (once Rei II’s most treasured possession) and as seen in End of Evangelion, wherein Rei III directly tells Gendo, “I am not your tool,” and subsequently joins Lilith. Rei III, representing the unification of the two split halves of Rei II’s soul in addition to the maturity experienced by Rei II (which explains why Rei III is significantly different from Rei I: both soul halves have experienced immense development and experience), kicks ass.
(In case you can’t tell, I love Rei. A lot. What a fantastic character and person.)
Follow-up and clarification! Please read!