I just finished Cryptum a few minutes ago actually, but i've been really studying all Halo's mysteries since the release of the first game, including ilovebees, the novels, secrets, and everything else...and i'll just say i think we're all amazed at the ingenious storyline bungie has created.
With huge mysteries such as this come great amounts of speculation, and that's of course all any of us are doing. So i have two theories, one pretty normal, and the second a little farfetched, but plausible.
The first possibility is that the Precursor captive is in some relation, the Gravemind. My personal thoughts have been that he is an infected Precursor. He is quarantined in order to stop the threat of the flood which would be genius irony because of the Forerunners defeating the Precursors in a secret two front war with the Flood just as they did to the humans. Sure, it's a possibility that they sent the ships of powder to destinations where they would presumably be discovered by Forerunners. But that really isnt very logical. A race as powerful as the Precursors (in my mind) would have a much better plan of action/retaliation than something so primitive. And as stated previously, why would they want to destroy their own Mantle?
Now, wrap your head around this. All these explanations are great and all, but the captive said "We meet again, young one. I am the last of those who gave you breath and shape and form millions of years ago. I am the last of those your kind rose up and ruthlessly destroyed. I am the last Precursor. And our answer is at hand." Now that would be pretty damn scary, im sure. But in reality, scary enough to lock away and place such protection over? Really, what caused the humans to put a timelock on this guy. Here we go: My theory is that the precursors are human. Sound crazy? It probably is, but hear me out. The similarities in the Precursors and Humans are undeniable. Irony was placed in some strange places, along with insinuations. The humans are the only ones who manage to figure out how to activate Precursor artifacts. The Didact himself communicates with the captive through HUMAN technology, not Forerunner. The humans figured out how to destroy the flood without the use of any Halos. The humans fiercely destroyed the flood and fought hard against the Forerunners on a two front war. Many instances show that the Humans are actually quite possibly stronger than the Forerunners, and moreso the true inheritors of the Mantle. Why are Riser and Chakas so important? Notice how those two are the key to saving the universe. Notice how dear the Librarian holds Humans compared to Sans-Shyuum, Sangheili, or even her own kind. Why can humans access Forerunner artifacts in present day Halo events, but not the Covenant or any of their races. What is so important about this race? The precursor is described as a "badly misshapen human"...maybe a Flood form. The Precursor claims the Forerunners rose up and ruthlessly destroyed them...but supposedly the Precursor artifacts are beyond the Forerunners means to even penetrate or harm...how could they be defeated by them...and why is this not mentioned before? The only race that reaches comparison of ruthless destruction are the Humans. The Forerunners ruthlessly destroyed them. The book closes with the Didact (Bornstellar) beginning his search for the humans (Riser and Chakas)....and the line "Our answer is at hand." I dont think he is referring to only the Flood. I think his answer is much to big for us to speculate on right now.