There's a lot of conflicting data within the forerunner trilogy about the Primordial. Some parts say it existed millions of years before the flood, and it itself says it IS Flood. The Lord of Admirals also thinks the earliest Forerunners must have imprisoned him, but it earlier says that humans communicated with him through Precursor lock technology, not Forerunner. And how would primitive forerunners lock him up in the first place? How can these things be reconciled?
My theory is that like the Forerunners deciding what to do with humanity, the Precursors were conflicted about what to do about the Forerunners who had risen up and mercilessly hunted down their species. Some had more extreme ideas, ideas to completely cleanse the galaxy and start anew. That would be the Primordial. His method for doing so was no doubt through the Flood. Like the Master Builder of the Forerunners, his ideas were too extreme, and he may have overstepped his bounds and so was locked up by his fellow Precursors, perhaps also with some forethought that if Precursors were ever wiped out, the dominant species would unlock him and thus they could have a sort of revenge in the end.
Now, what of his maybe control of the Flood while locked away? Precursors were said to be a transcendent species, above matter itself. I think that even in their powedered pre-flood form, they could think and communicate through the Organon, and were much more advanced at doing so than the Forerunners through the Domain. Thus in all the years they were (to us) inactive in the vials of powder, the Primordial convinced more and more of his fellow Precursors of his plan through their immaterial link through the Organon. They agreed upon this plan of slow infection to wipe the galaxy clean of those who would destroy them all, either to hand over the galaxy to the stewardship of humanity, or to eventually recalim it for their own - again, a parallel of how he corrupted Mendicant Bias over years of talk.
) as well as his messiah/god complex. ''
