The episode opens with Alex and Kara sitting in Kara's apartment talking about Kara's problems at work and Astra's death. Non barges into the apartment and asks Kara to come with him to Astra's funeral. Kara accepts and flies with Non far above National City where Astra's body is resting in a flying pod. Surrounded by the other Fort Rozz prisoners, Kara says a Kryptonian prayer and watches as Astra's pod floats off into space. Non says he will observe a period of mourning and then promises "the next coffin" will belong to Kara.
Back at DEO Headquarters, Kara tells J'onn and Alex that they have two weeks until Non comes back. Kara is acting particularly frosty towards J'onn (because she thinks he killed Astra) and is then called away because Maxwell Lord asked to see her. J'onn refuses to let Alex tell Kara the truth about Astra's death, because he doesn't want Kara to "lose" Alex too.
Maxwell Lord tells Supergirl he thought saving her life would get him an early release, but Supergirl still thinks he's a threat. Lord gets angry and says that he gets dangerous when he's bored, but Supergirl tells him to watch the Netflix the DEO had installed in between episodes.
Kara arrives at CatCo and discovers that Cat has hired a second assistant, Siobhan Smythe, because she's still upset at Kara for dumping Adam and skipping work last episode. After assigning Kara to watch the phones, Cat calls Lucy and Jimmy into her office to investigate Max Lord's apparent disappearance. After the meeting, Jimmy pulls Kara aside in private and tells her that the DEO holding Maxwell Lord without due process isn't right. Kara takes the DEO's side since Max tried to kill her with Bizarro, but she doesn't have a retort when Jimmy says that Supergirl's ethics might be compromised.
The DEO try to bring in an escaped Fort Rozz prisoner, but they discover that someone has already chained him up in a warehouse. A man in an advanced alien suit arrives and takes out the DEO team before flying away.
Alex and J'onn discuss the new player before Kara comes in and demands to be included in the investigation. While they don't recognize the man in armor, J'onn suggests they check with local law enforcement to see if any of their missing persons cases matches with missing Fort Rozz prisoners.
Speaking of the man in armor (who calls himself the Master Jailer), he executes the Fort Rozz prisoner with a laser guillotine.
Alex and Henshaw head to the National City Police Department for information. It turns out the National City PD has a file on the Master Jailer, since he's been dumping bodies by a river for months. They also meet a gruff detective named Warren who pretends not to be interested in helping but lingers outside suspiciously.
Back at CatCo, Siobhan calls Kara out for her flirty relationship with Jimmy and causes Kara to lose her cool in front of Cat. Before Kara can collect herself, Alex calls her and asks her to come to the DEO headquarters, which leads to more sniping by Siobhan for Kara slacking on the job.
Meanwhile, Lucy tells Jimmy that she's found out that Max Lord is probably being held by a secret government organization that tracks aliens. Jimmy lets it slip that he knows about the DEO, which leads to Lucy getting jealous about his relationship with Supergirl.
Back at the DEO headquarters, Alex and J'onn realize that the Master Jailer is targeting prisoners by their prisoner number. When Master Jailer tracks down his next victim, Supergirl arrives just in time to stop him. Supergirl and Master Jailer fight to a standstill, but he escapes with the prisoner after temporarily chaining Supergirl up.
Later that evening, Cat comes upon Jimmy brooding at one of the CatCo balcony and correctly surmises that he's conflicted about the Max Lord story. She tells him about a time that she caved to pressure not to write about an actor who abused his wife and that three months later the actor shot him. She says that journalists tell the truth, not because they want to be good journalists, but because they want to be good people.
Back at the DEO headquarters, Kara snaps at J'onn before Jimmy Olsen shows up unexpectedly to talk to Kara about the DEO unethically holding Max Lord. He says that Lord is terrified of Supergirl and that she needs to be better than Lord to prove him wrong. Kara doesn't appreciate the lecture and asks if Lucy told Cat about the DEO. Jimmy tells her that it was actually Siobhan and that Kara should look out for her new rival assistant.
Alex interrupts Jimmy's ethics lecture to tell Kara that the Master Jailer was actually Detective Warren, the suspicious National City cop from earlier. When Alex and Supergirl confront Warren, Warren's partner shoots him and Alex before his Master Jailer armor forms around him.
Alex wakes up (she was wearing a bulletproof vest) and finds out that the Master Jailer kidnapped Kara. Kara wakes up in a cage and discovers that her powers are missing thanks to a red sun. She talks to the Master Jailer's other prisoner for a bit before the Master Jailer arrives to execute the prisoner.
Alex realizes that the Master Jailer was a guard at Fort Rozz and tracks him to a remote cabin outside of the city. When the DEO moves in on the cabin to rescue Supergirl, they find that it's empty. However, Alex looks under the floorboards and sees the Master Jailer's ship under the cabin
Meanwhile, the Master Jailer prepares to execute the Fort Rozz prisoner and says that he has to kill Supergirl next. Before he can execute the prisoner, Alex barges in from the ceiling. Alex and the Master Jailer fight and Alex shoots out a portion of the ceiling to let some sunlight shine on Kara, which brings back her powers. Supergirl busts out the cage and quickly defeats the Master Jailer.
After returning the Fort Rozz prisoner to the college that he was taken from, Kara and Alex free Max Lord. While Kara thinks that Lord will keep the DEO's secret because of his "better angels", Alex says that if he does whistleblow on the DEO, she has a file with all of his crimes ready to be released to law enforcement.
The next morning, Kara snaps when Siobhan snipes at her again at work. Siobhan says she's not working for CatCo to make friends, she's trying to become the next Cat Grant, but Kara says they'll see who Cat decides to keep.
When Kara thanks Jimmy for his multiple ethics lessons, Jimmy says that Lucy caught him lying and that in order to fix things, he needs to tell Lucy the truth about Supergirl and Kara being the same person. However, things are left a little unclear what he's going to do next.
While discussing the episode's events with her mother's AI system, Kara asks about "Myriad" but the AI freaks out and threatens to self-destruct. J'onn shuts the AI down, but Kara's still not ready to forgive him and says that she can't work with him anymore.