In the Mirror Universe, where the Terran Empire rules with an iron fist, a young Philippa Georgiou returns home after surviving a dangerous competition to secure the title of Emperor. During this contest, she formed a connection with a boy named San, and together they emerged victorious against their peers. However, in a bid for power, Georgiou makes a shocking decision to sever all links to her past life by poisoning her family, a chilling act that signifies her ruthless ambition. As imperial officials arrive, accompanied by San—who has his own dark past—Georgiou takes control and enslaves him, marking the beginning of her reign.

Jumping to the early 24th century in the Prime Universe, agents from Section 31, an elite secret division of Starfleet, are dispatched to the Baraam space station, which lies just outside the Federation’s jurisdiction. Here, Georgiou, who has crossed over into this universe and has briefly served in Starfleet, takes on the guise of proprietress “Madame du Franc”. She is persuaded by Section 31 agent Alok Sahar to join his diverse and unconventional team, which includes Melle, an enchanting Deltan; Quasi, a shape-shifting Chameloid; Zeph, who wears a mechanical exoskeleton; Rachel Garrett, a seasoned Starfleet officer; and Fuzz, a microscopic Nanokin piloting a robotic suit resembling a Vulcan. Together, they are tasked with intercepting arms dealer Dada Noe on Baraam. In a clever move, Georgiou attaches a “phase pod” to a weapon Dada is selling, ensuring that only those with phase pods can touch it. However, the situation turns deadly when a masked figure using a phase pod steals the weapon and kills Melle. This weapon, known as the “Godsend,” is something Georgiou recognizes all too well, as she had initiated its development in the Mirror Universe—designed with devastating capabilities.

As the plot unfolds, Alok gains Georgiou’s confidence by sharing his traumatic history: he comes from the 20th century, where he witnessed the brutal murders of his family during the Eugenics Wars at the hands of the genetically-enhanced warlord, Giri. Alok’s past is entwined with violence and manipulation, having been forced to commit heinous acts on her behalf. They interrogate Dada Noe in a secure Section 31 location, unearthing crucial information. Dada reveals that he is a native of the Mirror Universe, having stolen the Godsend from a weapons facility, with intentions to sell it to the Terran Empire, which is scheming to invade the Prime Universe via a wormhole.

However, chaos ensues when their safe house is sabotaged and their ship is obliterated, making them suspect that they have a traitor among them. As tensions rise, Zeph goes missing, prompting doubts about his allegiance, but soon they discover his lifeless body. Furthermore, evidence suggests that Garrett may be linked to his demise. With keen intuition, Georgiou deduces that Fuzz had infiltrated Zeph’s exoskeleton, coercing him into sabotaging communications before forcing him to take his own life, while manufacturing evidence against Garrett. In a shocking revelation, Fuzz is transported away but not before disclosing that San—who Georgiou presumed dead—was behind the mask.

Determined to put an end to San’s plans, the team commandeers a derelict garbage scow to track him down. Quasi and Garrett manage to disable San’s shields using the scow’s tractor beam, allowing Georgiou and Alok to beam onto his ship. A fierce confrontation arises as Alok battles Fuzz’s mechanized suit while Fuzz himself attempts to attack the scow directly. San, fueled by vengeful ambition, aims to annihilate the Prime Universe with the Godsend, hoping to establish his own empire ruled by what he calls “righteous mercy,” contrasting sharply with Georgiou’s cruel regime. A brutal fight breaks out, leading to an unexpected activation of the Godsend. In a last-ditch effort, Garrett improvises by rigging an explosive using garbage from the scow, which Quasi launches into space, seemingly eliminating Fuzz. In the midst of the chaos, as San lunges to kill Georgiou, he tragically stabs himself instead, resulting in a poignant moment as he breathes his last in her arms. To thwart the impending disaster, Alok and Georgiou make the ultimate sacrifice, setting a course through the wormhole with the Godsend aimed at the Mirror Universe. However, just in time, Quasi transports them from the ship, saving them from the explosion’s wrath.

Three weeks later, the surviving members of the team regroup at Baraam. Among them is Fuzz’s spouse, Wisp, who pilots an identical Vulcan robotic suit and remains convinced that her husband survived the explosion. A mysterious communication from “Control,” the enigmatic director of Section 31, emerges as the group is briefed about their next mission, which awaits them on Turkana IV, foreshadowing further perilous adventures ahead.