: I read it only once, so I could be wrong, but I believe Silentium addresses
: this. As he was preparing to fire the rings, the IsoDidact posed this
: question to 343GS. It can be assumed that 343GS mistook the Master Chief
: for his old friend on account of being driven mad by loneliness.

In context with the Forerunner trilogy, I guessed that it meant that the Master Chief was clearly meant to be carrying the gene imprint of the IsoDidact himself, and is the human reincarnation of humanity's worst foe redeemed as its greatest defender.

I suppose we'll see if that turns out to be true.