User blog comment:Weedle McHairybug/So, why did Big Boss react with confusion in regards to Cipher? (Spoilers)/@comment-188.81.208.66-20120324171006/@comment-1672596-20120324171437

Yes, but that still doesn't explain why he still reacted with confusion even when Paz flat out explained their history to them, even explicitly attributing The Boss's vision as the source of its creation. Since he was one of the two men, it should have been easy for him to put two and two together after hearing Paz's story, yet even with Paz reciting its history to him, he was still confused. Here's the history recitation part, BTW:

Paz/Pacifica: Once upon a time. There were two young men who idolized a hero called The Boss.

One day, they suddenly lost the point of origin - The Cipher - that was like a mother to them.

Unable to come to terms with their sorrow, they each decided to carry on the will of their hero.

But they could not agree on what that meant.

In the end, they became bitter enemies, and the Zero from which they both started was split into two.

Naked Snake/Big Boss: Huh?

Paz/Pacifica: ...And you have been on the wrong path ever since.

There is no "Happily ever after" waiting for you in the end. Unlesss... You obey the will of Cipher!