Federation and food made from poop. But by far the biggest threat to Starfleet in the future is the Emerald Chain - a new alliance of planets somewhat less ethical than the Federation, dabbling in slavery, aggression and planetary interference. At the forefront of the Chain's expansion is the ruthless Osyraa - a figure whose name inspires fear throughout the post-Burn galaxy.
Osyraa finally infiltrated Starfleet HQ in Star Trek: Discovery season 3's penultimate installment, taking command of the Discovery itself (with ridiculous ease, some would suggest) and strolling right through the front gate like a futuristic Trojan horse. However, Osyraa's intentions perhaps weren't as evil as many assumed. Instead of going on the attack, Osyraa proposed a peace treaty, which iral Vance itted was beneficial to both parties. In fact, Vance's only sticking point was that Osyraa wanted to front the Emerald Chain herself, rather than standing trial for the crimes committed on her command. On this single issue, the Federation and Emerald Chain hit an ime.
This creates a moral quandary for Starfleet in Star Trek: Discovery season 3's finale. Usually, Starfleet now has a duty to uphold that principle by bringing Osyraa to justice in the courtroom - not just setting phasers to kill. Vance narrowed his troops' options even further when he said to Osyraa, "I can promise you justice" and spoke of his mission for "moral clarity."
The second major reason why killing Osyraa isn't an option for Starfleet is the structure of the Emerald Chain. The exchange between Vance and Osyraa makes clear that the Chain has other commanders, and wields extensive influence over numerous peaceful planets. This isn't the classic Star Trek situation where killing the main villain solves everything - Osyraa's death won't end the Emerald Chain, and can only worsen the already rocky reputation of the 32nd century Federation. Instead, Starfleet need a defining moral victory. Defeating Osyraa, taking her prisoner, and giving her a fair trial will send out a positive message about what the Federation stands for, and will bolster Starfleet's authority at a time when many, like the Vulcan and Romulan alliance of Ni'Var and the people of Kwejian, view them with suspicion.
The potential fly in the ointment could be Michael Burnham. Since reuniting with her crew in Star Trek: Discovery season 3, Burnham has been on a completely different page compared to her friends, ignoring orders, getting a demotion, and going rogue at every opportunity. Sometimes Michael's insubordination has proved to be the right call, but this new attitude has carved a divide between Burnham and her friends nonetheless. This growing tension could finally erupt in Star Trek: Discovery season 3's finale, with Starfleet wanting to keep Osyraa alive and deliver justice the right way, but Burnham choosing to disobey and kill the villain.