Star Trek: Discovery season 3 has provided several clues to suggest that Michael Burnham is poised to leave Starfleet. Discovery season 3 is set in the 32nd century, and while all of the crew have faced challenges in the future, Michael is the character who has perhaps been through the most so far. Jumping separately from the USS Discovery in the Red Angel suit meant that Michael ended up alone for a year before she was reunited with Discovery, a year that changed her as a person and as a Starfleet officer.
The Federation's decimation because of The Burn has caused Michael to become obsessed with finding the source of the event, but her methods have become rougher around the edges by virtue of learning to survive in a more lawless galaxy. Ever since Michael has reunited with the USS Discovery crew, viewers have seen her struggle with reintegrating into the rigid Starfleet command structure. Season 3, episode 6, "Scavengers," is perhaps the best example of this, showing Michael disobeying a direct order from Captain Saru to go off on a rescue mission to save her friend Cleveland "Book" Booker. Ultimately, Michael's decisions in "Scavengers" get her demoted, when Saru is forced to fire her as his first officer.
In perhaps the most telling moment of the series so far, Michael dejectedly takes off her comm badge after Saru demotes her, the gesture and her expression indicating just how disillusioned she seems to have become with Starfleet after what has just happened. While Michael still has good reasons to want to stay connected with Starfleet and seems committed to finding the cause of The Burn in an effort to help rebuild the Federation, there are a number of things so far in season 3 to suggest that she will eventually part ways with Starfleet and strike out on her own.
Michael Never Wanted To Join Starfleet
Despite Michael's continued commitment to Starfleet ideals, season 1 of Star Trek: Discovery revealed that Michael initially had no real interest in joining Starfleet. After her parents were supposedly killed by the Klingons, Michael was taken in by Ambassador Sarek and his wife and raised on Vulcan, where she attended the Vulcan Science Academy and had aspirations to join the Vulcan Expeditionary Group along with her foster brother, Spock. Ultimately, because of a decision made by Sarek about which of them would be allowed to join, Michael was rejected from the Group because of her human heritage, and only reluctantly joined Starfleet at Sarek's urging. She was placed on the USS Shenzhou under Captain Philippa Georgiou and eventually became Georgiou's first officer, beginning to thrive in Starfleet before the onset of the Klingon War.
Despite what happens later, season 1, episode 2 of Discovery makes it clear how little Michael wanted to join Starfleet in the first place, showing the audience her reluctance and even disdain for the organization in a flashback to her arrival on the Shenzhou. As seasons 1 and 2 of Discovery progress, Michael's feelings evolve, and that reluctance falls away, but the fact that she initially had no interest in Starfleet remains. This fact could certainly come into play in the future, as Michael continues to evaluate what she does and does not want from her life. If Michael is having doubts about whether or not she wants to be part of Starfleet, the fact that she joined under some duress from Sarek could potentially foster lingering resentment she might have about the choices made for her and could contribute to her decision to leave.
Michael's Authority Issues Have Resurfaced In The Future
Despite her eventual commitment to Starfleet as a career path, Michael has consistently chaffed against the rules and authority imposed by the organization. This manifested itself most strongly in season 1 when Michael was responsible for a mutiny aboard the Shenzhou after a disagreement with Captain Georgiou about the best way to approach contact with the Klingons. Michael was tried and convicted for mutiny after the event, becoming the first-ever Starfleet officer to be court-martialed for the offense at the time. While Michael is given a second chance when she joins the USS Discovery, she continued to demonstrate a willingness to at least bend and sometimes break the rules throughout season 1. Her defiant streak was a bit less pronounced in season 2 but seems to have come back with a vengeance in season 3.
Michael got a taste of life without Starfleet during the year that she was separated from Discovery in the 32nd century. Now that she is back with the ship, she is more used to doing things in a less rigid way. This has caused more than one problem between her and her captain so far in season 3. While Michael initially agreed to be his First Officer, the two have struggled to trust each other; Captain Saru has tried to keep Michael in line with Starfleet rules, while Michael has continually tried to get around them. This culminated in "Scavengers" with Michael's demotion after her unsanctioned rescue mission. With the consequences of her actions catching up to her once again, it is clear that Michael is struggling with the rules and regulations being a Starfleet officer imposes on her. If "Scavengers" is any indication, she seems to be on the verge of deciding that those rules are too high a price to pay, even if she still believes in Starfleet ideals.
Michael May Choose Romance Over Duty
Michael's past romance with Ash Tyler was cut short at the end of season 2, but in season 3 she has found a new and arguably better romantic partner in Cleveland "Book" Booker. Book and Michael met almost immediately upon her arrival in the future, and after some initial hostility to the two became close and developed a friendship during the year Michael spent looking for Discovery. Michael adapted very well to Book's lifestyle as a currier, clearly seeming happy while working with him. "Scavengers" also showed the beginnings of their romantic relationship, the two sharing their first kiss after Michael rescues Book from the Emerald Chain.
While Michael's relationship with Tyler was always fraught, she and Book seem extremely solid already. Their romance is built on a trust and affection that is obvious in all their interactions. Book makes Michael happy, and this coupled with how well Michael adapted to being a currier has shown her that there could be another life for her out there, one that she arguably enjoys more than her life aboard Discovery. Michael has already disobeyed Saru's direct order to rescue Book from the Emerald Chain, showing her willingness to prioritize him over her duties as a Starfleet officer. If their romance continues, there might come a time when Michael is forced to choose between Book and her duties, and from everything she has demonstrated so far in season 3, it is more than likely that she will choose Book.
Taken on their own, any one of these reasons might not be the deciding factor in Michael's eventual decision to leave Starfleet. Taken together though, they paint an obvious picture of why Michael seems to be feeling like it is time for her and the organization to part ways. Of course, if she did decide to leave, Michael has demonstrated that she is committed to finding the cause of The Burn, meaning that she would still be involved with Starfleet and Discovery's crew through her search. Michael resigning her commission however would mean that season 3 of Star Trek: Discovery could explore a much more expanded storyline for her, something that could end up being very interesting to watch.