Admiral Cornwell joins the fugitive Discovery and questions Spock. She shows Pike the footage of Spock killing the doctors at the psych facility. She expresses concerns about Section 31's Control program and Admiral P'Tar, a logic extremist who is in charge of it.
Airiam reviews and culls her memories. Tilly enters and they discuss Airiam's weekly memory review. It turns out Airiam was human and was in a shuttle crash that killed her husband. They had just gotten married on holidays.
In Engineering, Stamets is checking over the spore drive for the corruption. Burnham and Spock examine a map of the Red Angel signals. Their discussion distracts Stamets and he asks them to leave.
While decrypting files, Airiam has another flash of being controlled by something else and stops interacting with Tilly briefly. She deflects inquiries and redirects Tilly elsewhere.
On approach to Section 31's headquarters, they discover it is surrounded by mines despite the Federation's prohibition on the use of mines.
Burnham brings Spock back to her quarters and challenges him to a game of chess.
Nhan interrupts Airiam's work to tell her Tilly is looking for her. When Nhan asks what she's doing, Airiam asks about the augmentation Airiam uses to breathe the ship's atmosphere. The external control desists and Airiam returns to the bridge. Tilly informs her that the decryption isn't working anymore. Airiam asks Tilly to stay close while she works.
Cornwell gives them a route through the mines but informs them they must approach with shields down.
The chess game is irritating Burnham as Spock doesn't take the logical route. As she confronts him, he strikes back with the truth of her parents' deaths. They argue and Spock overturns the chess board. He leaves. Burnham is called to the bridge. A red light appears as she leaves the room.
As the Discovery enters the space around the headquarters, the mines start to move and attack the ship. They take evasive maneuvers and Airiam is taken over again. She sends Tilly away which confuses her and gains Nhan's attention. While others are looking away, she resumes the download she started in the other lab.
As the mines seem to be anticipating their moves, Burnham suggests that it's playing a game so they begin randomly calling out evasive maneuvers to introduce chaos to the gameplay and confuse the controlling system. The mines cease attacking and the ship is hailed by Admiral P'Tar who informs them that the order to attack came from Starfleet Command and that they will be arrested for treason.
Stamets and Spock work together in Engineering to get systems running to prevent being boarded.
Burnham, Nhan, and Airiam are tapped to infiltrate Section 31's headquarters. They find signs of a struggle in the corridor. Nhan steps away to get power restored and Burnham and Airiam find many bodies floating above them. Once gravity is restored, they fall to the ground shattering as they are frozen. One of the bodies is Admiral P'Tar and she's been dead at least two weeks, along with all the other Admirals that run Section 31.
Saru is able to shed light on both P'Tar and the incriminating Spock video. In both cases, holograms were used. The conclusion is that Section 31, in the form of the Control program, framed Mr. Spock.
Listening in, Tilly realizes that Airiam is the reason Control has allowed a boarding party. All of Airiam's personal memories were uploaded into Discovery's memory banks. Pike orders TIlly to find out what Airiam downloaded in place of them. The ship contacts Burnham and Nhan and asks what Airiam is doing. When informed that she's trying to restore Cornwell's control to the system, they are warned that she isn't doing that and they must stop her. Airiam hears the order, turns, flashes the sign she's been puppeted again and draws her weapon on Nhan and Burnham. Attacking Nhan, she pulls the breathing apparatus out. She overpowers Burnham who manages to break away long enough to force Airiam into an airlock.
The crew on the bridge figures out that Control wants the Sphere's information about AI in order to gain sentience and evolve. Tilly communicates with Airiam and manages to break through to the human side of her and Airiam tells Burnham to eject her out the airlock otherwise Control will force her to open the doors, kill her, and complete the download.
Despite her hesitancy, Burnham manages to eject Airiam before the doors open. Airiam warns her, just before she is ejected, that she must find Project Daedalus. As her system shuts down in space, Airiam relives her memory of walking on the beach with her husband.