Star Trek Villains Behind Latest Mystery Revealed

To really understand this wild theory, you need to first understand a bit about Section 31. This secret organization has existed since the very first days of Starfleet, and they are authorized to do whatever is necessary in order to protect the Federation from various threats. Accordingly, we know that Section 31 (an organization with no real oversight) has performed everything from routine assassinations to attempted genocide.

Section 31 played a major role in the second season of Star Trek: Discovery, but we haven’t seen or heard of them since the show jumped forward in time to the 32nd century. However, the most recent episode, “Jinaal,” featured a Trill scientist from the 24th century revealing that an unnamed Federation president recruited him and a team of five other scientists to research Progenitor technology. We have a pretty good idea of who this president is, and it’s someone who once had a Section 31 agent in his cabinet.

That same Trill, who mentioned the research team being assembled by a Federation president, said that the team ended up hiding their research thanks to the Dominion War. Based on context clues, this Federation president must be Jaresh-Inyo, someone we only saw onscreen in the Deep Space Nine episodes “Homefront” and “Paradise Lost.” While we never saw him again, a later episode, “Extreme Measures,” had Dr. Bashir discovering evidence that Jaresh-Inyo (no longer president by the last year of the Dominion War) previously had a Section 31 agent in his cabinet.

The Trill in Discovery was frustratingly non-specific about many things; for example, he outright refused to reveal the identities of the rest of the research team. Regarding why they decided to hide their research rather than give it to the Federation, all he said was that “the Dominion War was raging” and “everyone saw an enemy in everyone else.” The need for secrecy was doubly important because they “knew that technology could be used for great destruction.”

Buckle up like Deanna Troi has the helm because here’s my theory: this Trill and perhaps the other scientists became aware that the Federation president they were working for had a Section 31 infiltrator. This is a relatively amoral organization that tried to kill all of the Changelings with a fatal virus as a way of ending the Dominion War in favor of Starfleet. In short, if they were capable of such destruction with standard Federation technology, their capacity to do evil on a galactic scale would be infinitely increased with Progenitor technology.

Knowledge of a Section 31 infiltrator would provide a simple reason why the scientists hid their research: giving it to the Federation might very well have ended the Dominion War early, but it could have unleashed even greater horrors on the galaxy in the hands of Starfleet’s secret wetworks division. It’s even possible that Jaresh-Inyo knew about the infiltrator. After all, he went out of his way to recruit non-Federation personnel into the team, including a Romulan (who were enemies of the Federation even before it was formed) whose potential connection to the Tal Shiar (the Romulans’ own dirty tricks division) might have helped keep the findings secret even from Section 31.

So far, this is only a theory, but it would be fitting if Section 31, who was present aboard Discovery from the very beginning, played a part in the final season. Certainly, the existence of such dangerous technology is the kind of thing that Section 31 agents like Sloan would have happily killed for. To find out whether Starfleet’s dirtiest little secret will pop up again or whether the 32nd century will remain free of their influence, all we can do is keep tuning into this Progenitor mystery each week.