The events of this chapter took place after Chapter 40.
"Yui!" As Rei Ayanami watched Gendo Ikari rush toward Yui Ikari, whom Zero and Hikari had rescued together using the Life Solidifier, she felt as though something inside her had been freed.
As though a lock had clicked open.
After seeing Yui emerge with a face identical to her own, she began to reflect on herself.
So I was a copy of her...
The Commander made many copies. To him, "I" was replaceable.
But now he probably has no use for those copies anymore.
Then what am I now?
She kept pondering that question until the Commander summoned her to his office.
His face swollen, Gendo Ikari told her, "From now on, you no longer need to obey my orders."
Rei Ayanami asked him expressionlessly, "Is that another order?"
"You can take it as an order, or not."
"What matters is that you are no longer a tool or a vessel."
"Beyond that, I can't tell you much more. In any case, you're free."
After delivering those cryptic words, Gendo Ikari left Rei Ayanami alone in the Commander Room and walked out.
It was not that he was deliberately trying to sound profound. He simply did not know how to communicate with people, and now he also had to figure out how to explain this child to his wife.
If he failed to explain it properly, his face, which "Shinji" had already beaten to a pulp, would end up with a few more marks.
After briefly saying goodbye along the way to Shinji, who was leaving for another world with Zero, Rei Ayanami boarded the train back to her shabby little apartment. On the train, she thought about Gendo Ikari's words.
*He no longer needs me. I'm no longer his