Discovery, controlled by Osyraa and the Emerald Chain, is chased toward Federation Headquarters by the Viridian. Osyraa directs them to reduce firepower on Discovery to avoid significant damage to the Starfleet vessel. At Headquarters, Lieutenant Audrey Willa reports to Admiral Charles Vance that a communications jam is preventing contact with Discovery, and that the Viridian jumped through the mycelial network with them. Both ships also show residue consistent with being near the Verubin Nebula. Discovery, apparently under attack, is just a few minutes away from entering the shielded area, but Vance is hesitant to allow it entry.
On Discovery, Kanak reports that the ship’s bridge officers have been confined to the ready room and the rest of the crew placed in the brig. Most of Discovery‘s computer systems have also been converted to Chain software, but Kanak reports having difficulty deleting a particular section of code that, she says, appears to be “ancient Earth entertainment.” The program is using little memory, so Osyraa tells Kanak to ignore it. She also orders the Viridian to speed up so as to appear to gain on her. From a station on the side of the bridge, a display shows a pair of eyes watching the proceedings.
In the ready room, regulators attack Gen Rhys when he comments on the ongoing attack. Ensign Sylvia Tilly protests and asks them to release the rest of the crew, saying they need only her as acting captain for leverage. Zareh enters with Ryn and tells Tilly she should have killed him on The Colony instead of “leaving the job to the ice,” raising his left hand, which is injured and black. He mocks her leadership, noting it took very little time to hijack Discovery. He then tells the regulators that Osyraa wants the hostages, including Ryn, left untouched, and leaves.
Meanwhile, Michael Burnham and Cleveland Booker pilot Booker’s vessel through a transwarp tunnel, the same one they suspect Osyraa used to arrive at the Verubin Nebula so quickly. However, the passage is filled with debris and even Booker’s morphological ship cannot dodge all of it. Burnham says they are ninety seconds from Federation headquarters and warns of the remains of a Wanderer-class ship blocking much of the tunnel.
At headquarters, Discovery has entered the distortion zone’s gravity well; if they do not open the shields, it will be crushed. Vance orders the shields to open just enough for Discovery to enter and security to stand by. Will reports that Booker’s ship has exited subspace, confusing Vance. Their communications are fried, preventing Burnham from warning Vance not to allow Discovery in. Booker notes that Osyraa did something similar on Benthos IV, where she got behind the shields and then blew up the presidential palace. With just seconds remaining, Booker’s ship flies at high speed into Discovery’s shuttlebay, crashing in a fiery landing.
With the Viridian holding position outside the Federation Headquarter’s distortion field, Osyraa is angry that Kanak did not fire upon Booker’s ship before it crashed into the shuttlebay. Zareh reports that fire suppression protocols are blocking sensors, so they are unable to tell how many people were aboard, but that his regulators will handle whoever arrived. Osyraa orders him to keep any intruders alive.
Arriving in engineering, she greets Invigilator Aurellio, a wheelchair-bound Human scientist working for the Emerald Chain. He expresses awe that the spore drive is 930-year-old technology, saying it must have been a “golden age of science.” He reports that it is clear Paul Stamets is a conduit that allows Discovery to navigate the mycelial network but that he will have to perform a bioanalysis to learn more. He asks if engineering is a safe place to work, and Osyraa assures him she would never allow him to be harmed. Aurellio says she nonetheless seems worried. She tells him she is in hostile territory, about to take the gamble of her life. Aurellio tells Osyraa she would improve the galaxy by spreading the spore drive technology and freeing ships from having to use dilithium. She asks him to work fast and puts on an Andorian opera before leaving.
In the shuttlebay, DOT-23 drones have nearly extinguished the fires on and around Booker’s damaged ship. Booker reports that Grudge is “safe and secure” and gives Burnham another dose of radiation medication which causes lesions on her face to heal.
Burnham says their first goal should be to find Stamets, as Osyraa cannot jump the ship without him. However, Booker tells her she will have to act alone; he has just one device that can conceal her life signs from sensors. Burnham suggests that they still stick together, but Booker disagrees, arguing that they will expect to find at least one pilot and that Burnham is more familiar with Discovery, and thus better able to move about without being detected. Burnham confesses she’s in love with Booker ; he says he loves her too, they kiss, cue violins, etc..etc.. Burnham departs just before Zareh detects Booker’s life sign, and orders him taken alive.
At headquarters, an officer reports that Discovery is jamming transporters while Willa notes that the Viridian is simply waiting outside the shield perimeter. Vance wonders aloud why Osyraa would only bring one ship when she knows part of the fleet is at Kaminar. Realizing that Osyraa has hijacked Discovery, Vance orders all Starfleet vessels to go weapons hot and prepare to fire on the ship.
Zareh escorts Booker to the ready room with the bridge crew and Ryn, and punches him in the stomach before leaving. Tilly looks at Booker, who silently indicates with his eyes that Burnham is also aboard somewhere.
At the memorial wall in a corridor, Burnham attacks a regulator who was trying to pry a badge off the wall. He manages to stab her in her left leg, but Burnham subsequently suffocates him with her legs. She pulls out the knife and uses the regulator’s combadge to attempt to beam away but is blocked by the jamming field. Her leg bloody, Burnham hobbles away.
The USS Song and other vessels take offensive stations around Discovery and Vance warns the fleet near Kaminar to brace for retaliation. Osyraa hails Vance via hologram. He directs her to surrender or be fired upon, but Osyraa apologizes for arriving under “pretenses” and asks to talk. She releases most of the ship’s crew on shuttles as a good faith gesture but holds onto the bridge crew for leverage.
In a Jefferies tube, Burnham uses a device to cauterize her stab wound. She hears over the combadge that Osyraa has left the ship for Federation Headquarters. She then issues a distress call to Gabrielle Burnham on Ni’Var, reporting on the situation and asking her mother for help. She then overhears that Aurellio is with Stamets in engineering.
Vance and Willa welcome Osyraa and several regulator bodyguards to Federation headquarters. Vance says that the Federation president has authorized him to negotiate for the release of Discovery and its crew. Vance notes that they will respond with force should the Emerald Chain initiate hostilities and escorts Osyraa to a conference room.
In said conference room, Rhys and Bryce are covertly tapping out communications in Morse code. One of the guards notices and orders them to stop, but they do not. Owo angrily tells them to stop, prompting Detmer to chastise her in turn. The ensuing commotion distracts the guards and the crew attacks and neutralizes them.
Booker asks what the tapping was, and they tell him all officers learn Morse code in their first year at Starfleet Academy. Rhys reveals he merely told Bryce via code to keep tapping, amusing Booker. Tilly is locked out of the computer, but Ryn offers to hack the system. Booker reveals that Hugh Culber and Saru remained behind in the nebula. Lieutenant Ina notes that they have little time left before succumbing to the radiation, but Booker informs them that Adira took extra medication down to them, buying some time. Tilly says they will jump back to rescue them after retaking the ship. She orders Bryce to monitor communications, Owo, Detmer, and Rhys to open a door leading to a maintenance shaft, and the rest to barricade the turbolift doors.
Osyraa asks Vance why the holographic Dr. Eli has joined their negotiations. He tells her they employ biometric lie detectors during such negotiations. Osyraa says she does not intend to lie, which Eli confirms. Vance asks to speak to the officers remaining aboard Discovery, but Osyraa instead turns to Eli and states that they are unharmed except from minor injuries, which Eli confirms. Osyraa brags that it was easy to take Discovery in part because Saru was not present and asks if he was sent to Kaminar. Vance ignores her question and asks what she wants. Osyraa says she wants the Emerald Chain to unite with the Federation, surprising Vance.
She says the Chain’s dilithium is running out but that her scientific resources could replicate the spore drive technology. Vance asks why she needs the Federation as she has already taken control of Discovery, and Osyraa says that despite its failures since The Burn, the Federation still represents hope to many while the Chain does not.
Kanak has discovered the regulator attacked by Burnham, and Zareh surmises someone else using a life sign concealment device must be aboard. He traces the regulator’s combadge to Burnham’s location in the Jefferies tube.
In engineering, Stamets has been handcuffed to a railing and Aurellio removes the neural locks that the Chain used to control him and force Discovery to jump. Awakening, Stamets notes they are listening to Andorian opera. Aurellio explains that Andorians make the best opera singers because their antennae increase resonance. Stamets remarks he would like to hear the performance in person someday, and Aurellio tells Stamets that Osyraa would surely want a scientist of his talents at her Science Institute. Stamets asks if Aurellio’s children like opera, noting that he has three silver piercings behind his right ear, an Orion symbol to bless the arrival of a new child.
Trying to connect with Aurellio, Stamets says he has a child himself, apparently referring to Adira. Aurellio tries to turn the discussion to the spore drive, but Stamets continues to talk about Culber, who he notes is in danger inside the Verubin Nebula. Aurellio speculates that the tardigrade DNA in Stamets is how he controls the spore drive, but Stamets tells him the species has gone extinct and cannot be replicated. He will have to be killed to extract it, but Aurellio assures him they instead will grow the tardigrade cells.
Kanak and other regulators are approaching Burnham’s position in the Jefferies tube. Ryn has gained access to ship’s systems and Tilly tells him to scramble communications to help Burnham. Meanwhile, Burnham ties herself to a railing inside the tube. Just as Kanak grabs her, Burnham uses a phaser to destroy a sensor, fooling the computer into thinking there is a fire. The ship’s fire suppression system opens the tube to space to remove the oxygen. Kanak, holding onto Burnham’s boots, is eventually blown into space. Burnham’s strap fails, but the exterior vents close before she is ejected. On the bridge, Zareh watches the dead Kanak floating in space. A barefoot Burnham emerges from the Jefferies tube and tells Zareh over comms that he will need more regulators, to the relief of Booker and the crew. Burnham ditches the combadge and runs off.
Vance presses Osyraa to make her point. She tells him that if they are to join forces, the Federation must send a message that the Chain’s culture is valid and ethical “by acknowledging that capitalism is already happening within the Federation.” She notes it has been eighty-seven years since anyone from the Federation visited Deep Space 253, a distant outpost. However, Deep Space 253 has been trading with a Chain mercantile for nearly a century, and that trade should be sanctioned, Osyraa says. The Chain should also be allowed to set up an embassy on the station. Vance protests, arguing that the mercantiles traffic in goods used for enslavement, and some even have open slave markets. Osyraa says she has submitted a charter amendment to the Chain’s congress to outlaw slavery. It has enough support to pass, though she had to expend a great deal of political capital.
Vance tells Osyraa they would also require the Chain to release Kwejian and other pre-warp planets under its influence. She says he is asking powerful people to give up significant income, but Vance retorts that she could explain it to them by hijacking their ships and breaking through their shields. Willa and a regulator arrive to deliver the news that the bodies of several regulators have been detected in space around Discovery. Osyraa, seeking to advance negotiations, provides Vance with a copy of a proposed armistice. Among other things, it would require the Chain to follow the Prime Directive moving forward. Osyraa commits to a fifteen-year walk-back of control over Kwejian and the other worlds, arguing that an immediate pullout would cause chaos. Vance sits down to read the full document.
In the ready room, Ryn says that he cannot block their life signs but can scramble them so that sensors show all life signs that have been on the ship in recent months, making it appear like there are thousands of people aboard, and allowing the bridge crew to move freely.
Ryn and Booker volunteer to remain behind to fight off regulators that come looking for them. Booker tells Tilly that she represents Burnham’s best chance. Ryn scrambles the sensors, confusing Zareh, as the rest of the crew escape.
In engineering, Aurellio assures Stamets that the regulators are well-trained and will sort whatever the problem is. Stamets notes Osyraa hijacked the ship and has taken hostages, including himself, but Aurellio says she is negotiating to bring spore drive technology to the entire galaxy. He tells Stamets that while he may not like her methods, she is “more than you’re making her out to be.”
Aurellio explains that his genetic defect would have left him dead long ago but for the intervention of Osyraa when he was ten years old. Stamets says he has seen evidence of the science she supports, such as the pesticide on Kwejian. Aurellio cites the pesticide as a triumph, but Stamets reveals to him she provided it to the Kwejian in exchange for hunting trance worms almost to extinction while threatening their population, concerning Aurellio. Stamets also reveals Burnham barely escaped one of Osyraa’s labor camps, further shocking Aurellio. Just then, Burnham arrives, stuns several guards and Aurellio, and frees Stamets from his bindings.
Meanwhile, regulators finally break into the ready room and begin exchanging fire with Booker and Ryn.
Pulling on a new pair of boots, Burnham says she must get Stamets off the ship, but he protests while reloading a new canister of spores into the drive so they can jump back to the nebula to save Culber and Saru. Burnham reveals Adira is also in the nebula, causing Stamets to become even more frantic. Unable to convince him, Burnham resorts to using a Vulcan nerve pinch to incapacitate him.
As Vance reads the armistice, Osyraa asks who Eli is modeled after. Vance tells her his image was computer-generated. He finishes reading and calls the armistice “very impressive,” noting it made many concessions. But he has one further question: Who would represent the Chain to the Federation? Osyraa agrees that her reputation precludes her from being the diplomatic representative and that she would choose someone appropriate, perhaps a well-respected scientist.
She insists the person would be free from her influence, but Eli says it was a lie. Vance says that for the armistice to work, Osyraa would have to be tried for her crimes, shocking her. She tells him he is stuck in the past when she has offered a map to the future. “The past is the only light with which we can see the future,” Vance responds. Unable to agree on this final point, Osyraa walks away angrily.
Osyraa arrives back on Discovery‘s bridge, where Zareh, Aurellio, Ryn, and Booker are present. She chastises Zareh for losing the hostages, especially Stamets, though he protests that they must still be on board. Her harsh language and threats of violence unnerve Aurellio. He tells her there is no need for violence but she retorts that it is how progress is made, and Aurellio decides to stay. Osyraa tells Ryn to fix the sensors, but he refuses, saying he is no longer afraid of her. She puts her gun to his head, but Booker holds her off by saying he can show her to the dilithium planet. Osyraa guesses that it is in the Verubin Nebula, along with Saru, though Booker tells her the nebula is massive and dangerous and he can show her how to get there safely. Aurellio nods that she should accept the deal, but Osyraa quietly turns back and fires on Ryn at point blank range, disintegrating him. Booker is shocked, as is Aurellio, by the bloodshed. She tells him to produce a truth serum so Booker doesn’t lie about the planet’s location and orders the Viridian to start firing on Headquarters’ shields so they can depart.
Elsewhere, Burnham places Stamets in an emergency escape field and activates a homing beacon; she plans to eject him into space, where the Federation can tractor him to safety. Awakening, Stamets protests, arguing that Culber and Adira will die painfully if they do not return immediately. But Burnham says that Osyraa would use him to destroy what remains of the Federation. Leaving a phaser on overload near a window, Burnham exits the room. Stamets angrily shouts that they followed Burnham to the future so she would not be alone. The phaser explodes, rupturing the hull and pulling Stamets inside the escape field into space, where he is tractored to safety by the Federation. Burnham watches tearfully but regains her composure. Zareh arrives and holds her at gunpoint, telling her she will be sorry for saving Stamets.
At the armory, Tilly and the crew attack the guards and arm themselves. Tilly orders them to make it to the bridge no matter what, meaning fallen comrades must be left behind. They are surprised when three DOT-23 drones emerge. One displays an old Earth film, and Tilly realizes they are controlled by the Sphere data. The drones confirm her suspicions and offer to help take back the ship.