In the TV series specifically, Nguyen's actions (launching the protosoldiers to Mars specifically but more or less his entire story starting with when he takes control of the Agatha King) imply that he knows everything about the protomolecule plans. I must have missed when it became clear that he was privy to those plans.
In the first season or two he just seemed like someone interested in having a war and thus supported Errinwright, but I his final actions seemed to imply that he knew everything. When did that happen, and when was it revealed in the show?
If I understand it, the books do explain this (although I haven't read them), but they are sufficiently different from the series that I'd prefer series-only answers.