This scene explained the whole series. 5 core ideas
https://m.youtube.com/watch?v=ZKpFFD7aX3c
1. Neo wants to know why he's there. Architect basically says f you, you don't matter, someone else would have come along because of the imbalance Smith is creating.
2. Because he's been to Zion, had the traumatic unplugging, tasted real food and all that his head is scrambled so he will have difficulty understanding.
3. Smith is like an infection, even when he was plugged in he didn't agree with the Matrix and the architect wanted Smith dead all along.
4. Integral anomaly means anomaly that arose to destroy the accidental anomaly; Smith. Neo isn't Jesus, Buddha or Gandhi. He was basically Smith killing super soldier number 6. The architect spoke in such terms to not reveal to Neo that he was a pawn in a much grander scheme.
5. No one told him or no one knows; Neo sort of recognizes his place in the grand scheme but only really subconsciously.
The whole thing makes sense if you think of the anomaly as Smith.