The episode picks up six months after the premiere. Michael Burnham is on a prisoner transport ship to ship to a mining colony. Her reputation precedes her with some of the other prisoners.
There's a proximity alert as small organisms attach to the ship and begin draining it of power. The pilot goes outside the ship to deal with the problem, but her safety tether snaps and she floats away. The other prisoners panic, but Burnham.
A Starfleet ship, the USS Discovery, appears in front of the transport and draws the smaller vessel into its landing bay.
One of the prisoners notes that the ship is pristine, indicating it was just built. Commander Landry of the Discovery introduces herself and leads the prisoners inside.
Another prisoner notes a large number of silver science officer suits, indicating that the Discovery is a science vessel. They also noticed armed and armored guards with black badges, which none of them have ever seen before.
The prisoners are taken to the mess hall for food. Burnham sees one of her old Shenzhou crewmates, but she ignores her. The other prisoners attack Burnham, but she fends them off with Vulcan martial arts. Landry puts a stop to the brawl and tells Burnham that the captain wants to see her.
Burnham is brought to the bridge, where she finds Saru sitting in the captain's chair. She's brought to the ready room of Captain Gabriel Lorca. Lorca explains that he has an eye injury that makes him sensitive to light transfers. Burnham suspects that she is not on the Discovery by chance. Lorca suggests that the universe hates waste. He asks Burnham to help with an engineering project they have ongoing on the ship. Burnham refuses, but Lorca insists, saying that there are no free rides on his ship. He says he will use whatever resources are available to him to accomplish his mission, which is to win the war.
Landry brings Burnham to her quarters, which she finds pretty bare. Cadey Sylvia Tilley enters and finds her new roommate laying on her bed. Burnham swaps bads for her since Tilley has certain allergies. When Burnham tells Tilley that her name is Michael, Tilley jokes that she couldn't be Michael Burnham and then becomes frightened when she realizes she really is.
A "black alert" goes off on the Discovery. The lights dim. Liquid floats in the air. Tilley says she can't tell Burnham what any of it means.
Later, Burnham dresses for duty in a plain uniform with no badge. Saru greets her at her door and introduces himself as the Discovery's First Officer. Saru brings Burnham to engineering. Burnham comments that Saru's speech at Captain Georgiou's funeral was beautiful. Burnham struggles out an apology. Saru says that he believes Burnham is dangerous and worth fearing, but that Lorca does not fear things normal people do. She promises not to make trouble, but Saru makes clear that if she does then he'll do a better job protecting his captain than she did hers.
Burnham enters engineering. She's to report to Lt. Stamets. She's told he's in a classified area. When she remarks that Starfleet labs aren't classified, she's simply told that "this is Discovery." She tries to take a workstation next ot Tilley, but she's told they have assigned ships.
Stamets exists the classified area and puts a pod into a containment unit. Burnham and Stamets have a tense introduction and Burnham notices he brushes some silvery dust off his shoulder. He gives her some lines of code to reconcile and tells her to get busy, noting that they do not have assigned seats.
Burnham works until everyone but Stamets is gone from the lab. Stamets is discussing a joint project with a colleague over a video communication. He's interrupted when Burnham brings him the code and points out a mistake. He abruptly leaves her.
Burnham returns to quarters and finds Tilley snoring and drooling. She uses a napkin to collect some of Tilley's drool to get through the breath lock on Stamet's lab. She finds a garden of fungi.
Lorca receives an "above top secret" message alerting him that the Discovery's sister ship was destroyed along with all onboard while performing black alert maneuvers near Klingon territory. He tells Stamets to assemble a team, including Burnham, to collect material related to their project.
The team includes Burnham, Tilley, and Landry. On the transport, Tilley apologizes to Burnham, clumsily. Stamets and Burnham spar over science as Burnham tries to get up to speed on what they're doing. Stamets explains that there is no difference between physics and biology, that "physics has biology." Stamets resents Burnham for starting a war that co-opted allowed his and his now deceased friend's work to be co-opted by a warmonger like Lorca.
The transport docks at Discovery's sister ship. Stamets notes spiral markings on the ships hull. The ship is dark. They find bodies torn apart or bent in on themselves inside or turned inside out. Tilley finds a correlation with the markings. They notice a Klingon bat'leth. Stamets says if they "know about the device" its all over.
They discover a dozen dead Klingons, but their bodies aren't mutilated like the Starfleet officers. There are claw marks on the walls torn through reinforced metal. They find a living Klingon who shushes them just before being taken by a monster.
The team loses one soldier but makes it to the engineering lab and locks out the monster, for now. They investigate and gather the materials they need. They're trapped and need more time, so Burnham draws the creature's attention and starts crawling through the jefferies tubes. The creature follows, but Burnham, reciting Alice in Wonderland, drops down from the starship to the transport and they escape.
Later, Burnham reports to the bridge and has a moment with Saru, who admits she was always a valuable asset for Starfleet.
Burnham enters Lorca's ready room. Lorca invites her to stay on the Discovery. He says not to worry about Starfleet, that he's been given permission to win the war by any means necessary. She declines, and wonders why Lorca wants her there. She believes Lorca is building a biological weapon that is banned by war treaties and that he believes that she, as a mutineer, will do anything to get out of her imprisonment. Burnham says that she may not hold rank anymore, but she still lives life like a first officer of Starfleet.
Lorca tells her she's wrong and transports them both to engineering. He has her enter a sealed chamber. He pulls out a container of the spores that Stamets cultivated and releases them in the container with Burnham. Lorca explains that they're developing a biological fuel. The Discovery is behind on the curve, but the sister ship was traveling across the beta quadrant on them. They can be used for near instantaneous travel. He shows her by showing her various planets by activating the spores in the chamber. He believes this is the key to winning the war but can lead to much more after that.
He makes his pitch again, offering her a chance to end the war she helped start.
Saru, in the mess hall, sees the prison transport leave the Discovery and has a biological reaction.
Burnham returns to quarters and tells Tilley she'll be there permanently. Tilley is surprised to see an actual book among Burnham's collections. It's a copy of Alice's Adventures in Wonderland. Amanda Grayson, her foster mother, read it to her on Vulcan. It taught her about the limits of logic.
Later, Lorca thanks Landry for beaming their "new friend" on board. The monster from the sister ship is imprisoned on the Discovery.