A Star Trek: Discovery Theory
This is a theory about Star Trek Discovery. It may prove to be wrong, or indeed it may prove to be right. Either way there are spoilers for season 1 and 2, and potentially future spoilers. You have been warned
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Final Spoiler Warning
Here goes. I believe that Section 31 were fully aware of who Captain Lora was, not only that they were responsible, in part, for putting Lorca in charge of Discovery and training him in Starfleet protocol and procedure.
The big thing about “Mirror, Mirror” the TOS episode which introduced the mirror universe, was that it was easier for the landing party which suddenly found itself in the mirror universe to pose as savages, than it was for the savages to pose as civilised men. While Lorca is somewhat manipulative, he would have had to learn the true nature of Starfleet and the Federation, his prime universe counterpart’s friendships and affiliations, and finally how to be a Starfleet captain. In the meantime, there would have been an automatic hearing about the loss of the Buran, and the chance of psychological evaluation prior to him remaining in the fleet, let alone retaining command of a classified vessel.
Therefore, the first part of my hypothesis is that once the swap took place and the Buran was destroyed, Lorca was detained by Section 31, or Section 31 discovered who he was after being intercepted by Starfleet Security. While in Section 31 custody, he reveals his true nature, or enough about his true nature to lure them into complicity. A strong Federation counterpart, with a Klingon empire that has been vanquished, and a ship built on the ultimate technology (the Cheron). Section 31 was very keen to use this resource in the war against the Klingon’s. Lorca’s harder edge could be explained away by his stresses in war, and Section 31 could use their power to put him into place.
Therefore, Lorca manipulates a deal whereby he impersonates his counterpart and commands a ship, and leaves the Federation to victory in the war. In return, Section 31 agrees to find a way to return him home.
Lorca is a great believer in destiny, he would have therefore been vindicated when he discovered that the prime universe version of his chief lieutenant, Landry, was also in Section 31’s employ. She would have served as his handler, at first training Lorca in the ways of Starfleet. Meanwhile, Lorca is able to learn about Starfleet, particularly recent history, in record time. The Discovery in it’s initial incarnation as a science vessel, Stammets’ work with the Mycelial network, and of course, Burnham’s part in the war. This is of course everything that Lorca needs, a way home, and a new Michael Burnham to overthrow the emperor.
He manipulates it so that Saru and Detmer, two known associates of Burnham are assigned to the ship – giving the ship that sense of home for Burnham when he eventually gets her on board.
Let’s go back to Landry. She’s essentially on the crew as Section 31’s observer. Besides training Lorca, It would be her job to stop him from doing anything that threatens the Federation, or their plan. She poses as a member of Starfleet to keep on the bridge, and the assignment as chief of security gives her more reasoning to keep an eye on Lorca as the captain of the ship. However, thanks to his knowledge of his own Landry, he manipulates her into supporting his own plan to bring Burnham aboard.
I base the Landry aspects of this theory on the fact that Landry appears particularly harsh for a Starfleet officer. She’s happy to characterise the prisoners on the ship as trash. She seems willing to carve up the Tardigrade, and has little patience for standard Starfleet operating principles. She also appears to be fiercely loyal to Lorca.
The fact that Ash does not recognise the black badge means that at some point between “Context is for Kings” and around the time of “Choose your Pain” the “overt” Section 31 presence leaves Discovery. In the earlier episode we see one of these black badged officers standing guard when the prisoners arrive, and Tyler didn’t join the crew until after he was introduced in the later episode.
My guess is that Section 31 arranged for Burnham’s prisoner transfer, and the little accident that meant Discovery was so close by to save the day. Section 31 joined the ship to ensure that all had gone well, and there were no clues pointing to them (for example a counter espionage operation etc). They then either leave with the rest of the prisoners or by other means on some lay off.
With Landry dead, and Section 31 gone from the ship, Lorca was free to run things according to his own agenda, as they couldn’t risk destabilising Starfleet’s only proven weapon against the Klingons, the Discovery.
And that’s about it really. With their feet in the fire later in the season, Starfleet did exactly this when they used the Emperor to pose as the actual Georgiou and win the day against the Klingons.