iirc is the common theory is that episodes 25 & 26 for Shinji was him wondering if spoilers: whether to go fully with the human instrumentality thing or not while he was initiating the third impact. He ultimateley choose not to and thats why rei god started breaking apart and shinji + asuka woke out of the lcl. Presumably people who also wanted to remain would soon also form out the the lcl
they were introspecting because they had spoilers: all become lcl with the third impact, with only their psyche hanging on. Asuka was also thinking while she was hidden in the lake
sorry if most of it is wrong, I watched NGE 2 years ago