- "What I have done is protect this city. This world. Humans understand little about justice. Justice must be absolute. I'd hoped that you'd see justice the same way your mother did. The way I do."
- —Master Jailer to Supergirl
Supergirl does battle with the deadly Master Jailer, who is hunting and executing escaped Fort Rozz prisoners. Also, Cat hires a second assistant, Siobhan Smythe, who immediately tries to one-up Kara, and Kara and James disagree over the D.E.O.’s methods. 
An unknown figure flew through the night skyline of National City.
At home, Kara told Alex that she should probably go to bed with her missing work and all. Alex told her not to worried and hugged her. Kara admitted she missed Astra, and that she's almost getting through to her when she was killed. Alex was about to confess to killing Astra when they were interrupted by a noise by the window.Kara dismissed it as her being jumpy at first, but then Non announced his presence and asked Kara to come with him on behalf of Astra, which she agreed despite Alex's protests.
Up in the sky, the funeral for Astra was held. Non told Kara he would hold a period for mourning, and vowed to kill her after it was over.
At the D.E.O. headquarters, Kara told J'onn they have two weeks. After she left after Max demanded to see her, Alex told J'onn she could't lie to Kara about Astra's death any longer, but the latter insisted Alex was what Kara needed.
At Max's cell, he bargained for parole due to his help in saving Kara from the Black Mercy. She calmly refused and cited how dangerous he was, until he started to lose his polite exterior and yelled that she would be dead if not for him, but she countered that without him, the world would be a better place.
At CatCo, Kara was cheerfully informed by Cat Grant that she had hired a second assistant, Siobhan Smythe, and Kara was surprised Cat pronounced her name correctly. Cat designated Kara as "Assistant #2" to her confusion. Siobhan promptly one-upped Kara's coffee while Winn looked on uncomfortably. Cat told Siobhan to get James Olsen and Lucy Lane into her office and told Kara to cover the phone. Towards Winn, Kara feigned confidence over her rival and that she's not upset but Winn pointed out she just broke her phone, and walked away smiling in a slightly self-satisfied manner.
Using her super hearing, Kara heard Cat revealing her theory that Max is missing. Cat dismissed Siobhan and told Lucy and James to investigate.
James was about to talk to Kara but was interrupted by Siobhan, who tried to flatter him but was brushed off. When they were alone, James voiced his objection towards D.E.O.'s detainment of Max without due process. Kara told him it's not his place to worry about the D.E.O.'s ethics, but James said it's not D.E.O.'s ethics he's worried about. Siobhan saw them talking and walked away smirking.
J'onn briefed D.E.O. agents about a Fort Rozz escapee who went by Gabriel Phillips. When they found him, he's been chained up and begged them to help him. An armored figure appeared, shrugging off fire and retaliating with energy blasts before taking off with the escapee in tow. Alex told J'onn he was abducted.
Alex and J'onn discuss the mysterious personality when Kara came in, asking why they didn't call her. When J'onn said he thought she needed some time off, she bluntly retorted that she would request it if she needed it. They were unable to determine the attacker's identity or motive.
The armored figure was shown holding the alien prisoner, saying his human disguise could not fool him and demanded him to show his true form. He activated a guillotine despite the alien's protest that Krypton has no death penalty, as they were not on Krypton, and the alien transformed, asking to leave. He was told that "No one escapes the Master Jailer" and was executed.
J'onn and Alex went to the police in search for leads. One of the detectives apparently disliked Supergirl. An officer apprehensively told them there were at least five more cases of kidnappings that ended in decapitation, and that the victims were "weird" including one with gills.
At CatCo, Siobhan was eyeing Kara from her desk and decided to send her a message asking what's between her and James. Kara asked what she meant and she boldly sent another asking whether they were dating or friends with benefits, which Kara denied, while Winn observed. Siobhan continued sending messages and upset her when she apparently accused her of being "obsessed" with James. Cat arrived and told her to keep it down. Alex called Kara, who said she's dealing with a problem right now, but Alex told her it couldn't wait. Before she left, she tried to remind Siobhan Cat's lunch, but Siobhan recited it perfectly and mocked her for not doing her job, winked at Winn and smirked at his uncomfortable reaction.
Lucy showed James some car plates that she found out through her father that belonged to a secret government department that tracked aliens. James tried to dissuade Lucy from investigating further, closing the door on an eavesdropping Siobhan, but accidentally revealed he knew what the agency was - D.E.O. Lucy deduced that Supergirl told him about it, guessed he was even closer to Supergirl than Superman and stormed out.
J'onn and Alex figured out that their opponent was killing Fort Rozz escapees by their prisoner number, making his next target prisoner #2445.
Master Jailer confronted #2445, demanding him to show himself, and knocked him down when he attempted to flee before he was interrupted by Supergirl. Ignoring her question about his identity, he attacked her with chains, which she dodged by shooting into the air. They fought and Kara gained a slight upper hand. The Master Jailer managed to tangle her in chains, and by the time she burned her way out with heat vision, both him and the escapee has fled.
James was drinking on the CatCo balcony when he was joined by Cat, who knew something was troubling him and shared her experience with troubles that were both work and personal - back at the Daily Planet, she was finally assigned to interview a rising star of an actor. Everyone told her he's great, but his wife's makeup artist revealed the bruises she had to cover up every morning. She caved to PR pressure and did not publish that, but three months later he shot his wife in the head and Cat's been haunted by what she could have done ever since. She said they do what they do because they wanted to be good people. James saw Siobhan just behind her.
J'onn identified the Master Jailer's chains as of alien origin. He revealed #2445, real name Luzano, was a drug smuggler before Alura Zor-El put him away, which made Kara snap at him. Alex and J'onn decided to continue investigating, and James arrived wanting to talk to Kara. They argue further about Max's imprisonment and James pointed out people have a reason to fear her. When James questioned what kind of hero what she wanted to be, she replied she did what needs to be done, which greatly disappointed James. Kara asked whether Lucy told Cat about this, and James said Siobhan did.
Alex beckoned for Kara to come out. The baton the Master Jailer used to knock down his quarry was standard police issue, and they identified the DNA as the detective who hated Supergirl, Warren.
The two detectives were driving and discussing the missing aliens when they were stopped by Supergirl. Kara and Alex confronted Warren, who claimed to be one of the good guys. Detective Draper said he was telling the truth and shot both Alex and Warren. With a raise of his fist, his Master Jailer armor appeared over him. Alex was protected by her bulletproof vest, but he took Kara.
Kara found herself in a cage without her powers, while Luzano pointed out the artificial red sun radiation that was suppressing her powers. He declined to answer why he was in Fort Rozz at first, but then talked about his past leading to how he tried to get into drug smuggling for his ailing wife but was caught on his first run. When Fort Rozz landed on Earth, he only wanted a good life and taught his students about the stars, which reminded Kara of Astra. Kara promised to get them out of here, but the Master Jailer appeared and said she would not.
Alex told J'onn they only have twelve hours between Master Jailer's kidnappings and executions. Alex said they couldn't find a match in the prisoner files which may have been corrupted in the crash, but realized he was a guard. The D.E.O. apparently located him.
The Master Jailer told Kara he was continuing Alura's vision of justice, and prepared to execute Luzano. Kara begged him not to do it and he realized he would have to kill her too.
The D.E.O. searched the cabin where he was supposed to be, but found no one.
Luzano asked the Master Jailer to let Kara go, but he denied the request.
Alex noticed strange glowing from under the floor, pried the boards open and discovered Master Jailer's ship far below.
Kara asked Luzano to look at her but he was resigned to his fate. D.E.O. agents blew up the top of Master Jailer's ship and attacked him. He gained the upper hand and forced Alex onto the guillotine, but she fired more shots into the ceiling, allowing yellow sunlight to shine in and recharge Kara, who fought and finally defeated the Master Jailer.
Luzano asked what they're going to do with him. Kara brought him back to his school, saying he's served his sentence and he had students to teach.
Alex and Kara released Max from his cell and told him he's free to go. Kara tried to appeal to his better nature to his amazement. Once Kara left, Alex threatened him to never reveal their secrets or they would reveal his crimes.
At CatCo, Siobhan smugly told Kara she finished all her work for her. Fed up, Kara bluntly said she didn't like Siobhan, but Siobhan retorted she wasn't there to make friends, but to be the next Cat Grant. Siobhan detailed her massive ambitions, dismissively stating that Kara will be her own personal assistant one day. Undeterred, Kara challenged that they'd see which one of them gets to stay.
Kara thanked James for making her a better hero, and he returned the sentiment. He said he would need to tell Lucy the truth about Supergirl's identity if they are going to stay together and asked for Kara's permissions. He left when Kara didn't respond.
Kara told the Alura AI about Luzano and how they helped him in a weird way. She also asked about the "Myriad" Non and Astra were working on, but the AI warned it was not authorized to discuss it and further questions will result in self-destruction. Kara said the hologram used to remind her of her mother, but now she could only think of Astra and how J'onn supposedly killed her. Kara walked out, saying she didn't know how to work with him any more.
- The episode's title is a reference to what Superman is known for protecting: "truth, justice, and the American way".
- Master Jailer was originally introduced as a Superman villain in the comics.
- When J'onn suggested they could be dealing with an intergalactic bounty hunter, Alex begins to ask, "You mean like...?" and J'onn interrupted her to say, "If he were in town, we'd know". This is a possible reference to Lobo.
- Supergirl said "I thought masks were only big in that other city" which seems like a reference to Gotham City or Star City.
- Supergirl mentions that wanted to catch a corrupt cop ever since she and Alex binge-watched the television series, The Wire.
- Hank compares Jailer's suit to that of Robocop.
- Alex states "No, I didn't, here comes the sun" when Master Jailer points out she wasted her ammo. This is a possible nod to the Beatles song Here Comes the Sun.
- Winn refers to Siobhan as "Cat's new Mini-Me", a reference to the 1999 film Austin Powers: The Spy Who Shagged Me.
- When Max says he's bored, Kara sarcastically suggests that he should watch the television series Call the Midwife on Netflix.
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