A lot of ppl just assume that he was dropped off with the teacher guy right after Yui's death, and that was the last he saw of him, but if you really look at it, there are a lot of things that hint at a more complex narrative here.
I'll be talking specifically about the OG series timeline here, not the manga or the rebuilds which all have their own unique tweaks going on.
But there are a lot of hints scattered through eps 1, 16, 15 and 20 that are in a very fragmentary, out-of-context fashion with no defining statement/narrative, as is typical of early/ traumatic memories.
One angle that everyone picked up on (because it's hinted more clearly in 21 and explicitly stated later in EoE) is that Yui was the mastermind and stayed willingly ("but mother was smiling")
- Fuyutsuki mentions that Shinji and Gendo haven't seen each other in three years - three, not ten.
- We get the famous flashback of baby Shinji crying at a train station. The script notes that he's supposed to be "4 or 5" - not, as in the ep 21 depiction of the activation element, around 3.
-> He probably rode the train on his own which is how the train car came to symbolize 'hell' for him, cause his little self sitting there with his bag? That's the traumatic moment he is "stuck" in, so to speak. He experienced/conceptualized this as rejection & grew up building much of his personality around fear of rejection.
- We get some elaboration on the "three years" thing: Apparently when Shinji was about 10, they met up for the visit to Yui's grave & in went poorly, accumulating in Shinji "running away", and after that point, Gendo never showed up again - implying that, before this point there was at least intermittent contact. Not enough for Shinji to feel like he wasn't completely forgotten, but I'd assume he made the occasional courtesy visit.
- Shinji has a notable reaction when he notices Rei sitting in the heli
- "but you were the one who ran away!"
- Gendo (explicitly labeled as from 10 years ago): "You musnt't run away" (hinting that this is were he might've picked up the phrase)
- some newspaper clippings & the like of how Gendo apparently ended up on trial after the fatal accident (maybe Shinji accepted this narrative when he was older and bitter and went looking through the old papers for answers, but part of him remembers Yui being all excited about the experiment)
- the newspaper clippings also include the words "out of control" so it's possible that EVA 01 went out of control for a bit during it, like in ep 14 when unit zero nearly absorbs Shinji
Episode 20 - more or less where the penny comes as close to dropping as it ever does.
- at this point it's very much made explicit that Shinji always lowkey blamed him for what happened to Yui (this once, he's actually innocent)
- "that must be it, he left me cause Rei was there"
- then the 'you left yourself' point is reiterated, but more interesting, we get to see baby Rei, in that same sepia flashback hue, the exact same outfit, and she seems to be at the train station though that could just be about fitting her in the existing metaphor.
Now of course you could argue that they didn't want to come up with another design, but why make her appear as a child at all?
No, what this might suggest is that Shinji actually saw child Rei with his own eyes at some point.
- "No, that's not right I already knew EVA! That's why I ran away from father and mother"
- Shinji only shows up once or twice as a a cute happy toddler, but we get some further context like
- Mini Rei was around in 2010
- Yui was the mastermind & deliberately brought Shinji to the activation experiment, which he witnessed
- Gendo definitely actually cared about Yui & was super thrown out by her death to the point of just vanishing for a week
There's also this interesting bit from the same Q & A that gave us the name meanings (linked in the wiki)
5.2) What happened to Shinji when he was small? (ep.21)
He witnessed Yui's fatal accident, and "ran away" from NERV and his
father. Probably as a result of this and Yui's death, Rei is
recruited as a pilot. In the earlier episodes he has no recollection
of this. We were made to assume that Gendou abandoned him to work on
his project. Shinji finally remembers in ep.(20? 21?).
I don't think this justifies what Gendou does to his son, but that's a
If Rei was "recruited" (or rather, "made") as a result of Shinji leaving, you might almost conclude that they meant to use him first. I mean, Asuka is also just 5 or so when they first recruit her.
So here is how I would arrange this into a timeline:
- Shinji witnesses the activation experiment; Maybe there's a scary Eva reaching towards the glass (actually Yui orienting herself in her shiny new body). I like to picture that Shinji and Gendo somehow got splattered in LCL when they pulled out the now empty divesuit.
- Gendo goes missing for a week. IDK if Gendo took him with him or left Shinji with some relative but in either case it was a sudden chaotic disruption
- possibly during this time the salvage attempt took place. Fuyutsuki does something desperate that results in "salvaged remains" being recovered.
- Baby Shinji is considered as a possible pilot candidate. But the moment he sees the thing that ate his mom (or maybeit's Yui herself that he's scares of), he flat out panics; toddler tantrum ensues.
- Gendo is put on trial; Shinji overhears a lot of gossip about this.
- it's not until a good while after the experiment - maybe a whole year - that Gendo throws in the towel. He felt he just couldn't handle it & puts Shinji with the teacher guy.
- If you go by the bit from EVA 2 where Yui is the daughter of a SEELE member, he must've taken precautions to keep him out of their hands. From Shinji's perspective this must've looked like no other relatives were interested in him either
- they still need pilots so... Gendo turns to the biohazard container with the scrambled bits of flesh resulting from the recovery operation, and makes Rei, with the intention that she will pilot EVA 01.
- Kyoko's demise and Asuka's selection occur sometime after that - for Asuka to be the 2nd Child Rei must already have existed or at least have been planned for
- Shinji actually sees child Rei at some point - either at the train station (less likely - she wouldn't have been around yet? ) or (most likely) during the "3 years earlier" incident. Maybe that's WHY it went south - cause here comes a very bitter, 10 year old Shinji whos starting to develop some capacity to think for himself & he sees the father that hardly ever came to see him all those years show up with a strange girl that he apparently does have time for
- Rei gets injured days before Sachiel is due to show, but Gendo knows there's at least one person whom EVA 01 might accept...
- He has probably noticed the inconsistency that, the Rei he knows can't be the same girl from back then cause she'd be too young ... (just like there's no way she could have been at the train station in episode 1) but they look identical. Maybe he's awkwardly asked Rei at some point if she has a little sister, but mostly, like most unpleasant upsetting things he encounters, he tries not too think about it too hard
Though there is also the possibility that Rei wasn't created as a 4 year old, but as a baby. so she existed at the time of Asuka's recruitment, in some incubator down in terminal dogma, and grew normally until she was murdered by Naoko, the second one started middle school with Touji, Kensuke & the others, making 2014 the latest possible date for her creation, though it's likely that they just didn't send her to school before that.
It's unclear if she remembers anything from the first clone, kinda depends on when they figured out the memory transfer tech...
and it's just as likely that they did make her as a toddler so as to not to bother with any of that troublesome baby stage - but she would've missed out on the emotional learning & bonding that normally happens while people are babies.