Michael Burnham becoming captain was indicated quite early in Star Trek: Discovery (& Emperor Georgiou left the biggest hints)

Star Trek: Discovery showed Michael Burnham's steady growth from a First Officer to a Captain. While Burnham did not become Captain until season three, Emperor Georgiou predicted the future of her career.

While Emperor Georgiou and Captain Philippa Georgiou (both played by Michelle Yeoh) are essentially two different individuals, both had immense faith in Burnham's capabilities. While in the mirror universe, Emperor Georgiou had mistaken Burnham as her daughter and referred to her as Captain because Burnham's mirror counterpart was the Captain of the USS Shenzhou. Coincidentally, the same would happen in the prime universe a few years later.

Star Trek: Discovery had hinted at Burnham's future through Emperor Georgiou

When Star Trek: Discovery starts, Michael Burnham has already worked under Captain Philippa Georgiou for seven years. In that time, Georgiou has been more than Burnham's guide and mentor. She had become more of a mother figure. While their bond was special, Captain Georgiou ensured Burnham had the right training to become a Captain one day.

Before the events of Star Trek: Discovery, Burnham had already gone through a lot. She became an orphan when her parents, Dr. Mike Burnham and Dr. Gabrielle Burnham, were killed by the Klingons. Burnham's parents were killed because the Klingons found out that, as instructed by the Federation, the Burnhams were working on a suit that could be capable of time travel and had a time crystal. Burnham then gets adopted by Ambassador Sarek and gets trained at the Vulcan Learning Center and Vulcan Science Academy as a xenoanthropologist.

After graduating, she joins the USS Shenzhou under Captain Georgiou. In Star Trek: Discovery season one, episode two, the Shenzhou encounters the Klingons, and Burnham disobeys orders and tries to fire first to prevent war. Her actions fail, leading to Captain Georgiou’s death and Burnham killing the Klingon leader, accidentally turning him into a martyr. She is convicted of mutiny and is sentenced to life in prison. However, Captain Lorca recruits her to the USS Discovery for a wartime assignment.

In Star Trek: Discovery season one's episode titled "Despite Yourself, Burnham and the crew are transported to the Mirror Universe, where she impersonates her mirror counterpart, who was a Captain on the USS Shenzhou. Interestingly, Emperor Georgiou calls Burnham "Captain Michael Burnham, mistaking her for her mirror counterpart. This moment foreshadows Burnham becoming a Captain at the end of Star Trek: Discovery season three.

This minor detail also highlighted how, in both universes, Burnham and Georgiou share a special relationship (although mirror Burnham was conspiring against mirror Georgiou).

Burnham learns that Lorca is actually from the mirror universe and is conspiring against the Emperor. Burnham and Emperor Georgiou stop him, and Burnham brings Georgiou to the prime universe. In the prime universe, Burnham helps prevent a genocidal attack on the Klingons, choosing diplomacy instead of destruction.

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Burnham convinces L’Rell to end the war peacefully. For her actions, Burnham is pardoned, reinstated as Commander in Starfleet, and promoted to Chief Science Officer. As Star Trek: Discovery goes on, Michael Burnham becomes the Captain of the USS Discovery.

You can stream all seasons of Star Trek: Discovery on Paramount+.

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