The episode opens as a young Kara Zor-El makes her way through the Phantom Zone to Earth; just before her craft drags Fort Rozz behind it, a computer console in her dash lights up with the telltale three dots of Brainiac.
At her apartment, Alex brings doughnuts to Kara and tries to bring her back to the DEO, but Kara says she can’t work with Henshaw anymore, knowing that he killed Astra. Then she has to rush to CatCo.
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At the office, Siobhan is being terrible to Kara and James when Cat comes in to call a meeting.
Siobhan had intercepted one of Cat’s packages, which James opens. It’s a thumb drive, and a message that claims to have information from a hack that would reveal affairs by powerful people. Cat doesn’t want to publish the gossip, and instructs Siobhan to melt the thumb drive in the microwave.
At the DEO, Alex and Hank are sparring, with Alex clearly getting out of hand. Hank shape shifts into J’Onn briefly and tells her that if she’s angry, she needs to talk to him instead of punching him.
Alex admits she’s upset that Kara left because of the lie they told. Henshaw tells her that the DEO will be fine without Supergirl.
At CatCo, James tries and fails to convince Kara to let him tell Lucy about Supergirl.
A hacker takes over the in-office monitors at CatCo, expressing frustration that Cat didn’t out the cheaters with the evidence on the thumb drive. When Cat dismisses her, the hacker threatens to launch “the age of chaos” and signs off. Moments later, all the traffic signals in town turn green and Kara has to rush out and become Supergirl to save people in traffic.
As reports of the cyber attacks worsen, Cat calls a meeting. She tells Olsen to circle the wagons and get every investigator they have on the case.
James, instead, goes to his office and, much to Lucy’s chagrin, plans on tackling it with Supergirl.
At Kara’s apartment, Winn is having trouble trying to write a code to track the hacker. She appears on his computer screen, and then pops out of it, taking the form of a blue woman with the Brainiac symbol on her forehead. When she attacks James and Winn, Supergirl freezes for a moment but gets a rescue from Henshaw and Alex.
They tell her that they tracked something back to her computer, but can’t tell her anything more unless she comes back to active duty. She tells them to go ahead and leave.
On the outskirts of town, a young man is about to propose to his girlfriend. He’s recording it with his cell phone, which the blue-skinned hacker pops out of to scare them away. Moments later, Non arrives, and after some sexually-charged banter, they reveal that the hacker is called Indigo — formerly Brainiac-8. She tries to flirt with Non, who gets upset because she’s being disrespectful to Astra’s memory.
Indigo tells Non that Astra’s notion of living alongside the humans can’t work, and Non asks her what she’s done. Indigo says hell is coming to earth, and when it does, only she and the Khryptonians will survive it. She vanishes back into the waiting cell phone.
At CatCo, Siobhan is having trouble with the copier when Winn comes to help her with it. She’s upset because her father was one of the members of the cheating site that Indigo tried to out, then she leaves, asking him to make copies for her.
Alex comes to see Winn, asking him to help her disable the malware. Kara is visibly annoyed, but Winn goes to help anyway.
When Kara expresses her frustration with working without DEO intel and support, James suggests a place they can go.
Outside the Fortress of Solitude, James shows Supergirl the “key” — a super-condensed piece of drarf star outside the door that only a select few can lift. Inside, she passes a statue of Lara and Jor-El, and a Legion Flight Ring among other things, before getting to a computer where Kelex the Fortress robot tells her about Brainiac-8, the deadliest prisoner ever sent to Fort Rozz. James wants to tell Henshaw, but Supergirl says he’s all the help she needs.
At CatCo, James tells Lucy about what they learned at the Fortress, but she’s just upset that he missed a date with her to go be with Supergirl. She storms off, promising to tell her father about Indigo hacking the military. She stands on a balcony, pissed at James. Kara goes to try to console her, but all it does is upset her further, when it turns out the story James told Kara about his father giving him his first camera is something that he hadn’t ever told her before. Lucy tells Kara thank you, that it helped a lot.
Later, Kara says she misses Alex and Winn. Lucy comes to them to reveal she thinks the whole hack was about targeting General Jonathan Mathers — the only military official in town who has access to nuclear launch codes.
When Mathers makes his way to a secure location with no Internet access, Indigo pops out of his phone, killing or disabling everyone there and then stretching her arms to separate ends of the room to turn two keys at once, launching the missiles onsite. As she does so, Supergirl arrives and starts fighting with Indigo. Indigo manages to pin her down, watching the process unfold.
As the missiles launch, government is scrambling into action. Supergirl tries to catch up with the missile, worried there’s no other way to save the city other than for her to take out the nuke personally. Pushing the rocket out of the way won’t work, and Kara can’t use her heat vision because it might blow the missile. She calls in to Hank for help. Moments before the missile strikes the city, Hank manages to talk her through disabling the warhead, rendering it harmless.
At the launch site, Indigo is about to send additional missiles when Supergirl tackles her. Meanwhile, Winn is uploading a nasty computer virus he created to try and take out Indigo…but she reaches through a cell phone to strangle Winn at the DEO desk. As she monologues, though, Winn deactivates her with the virus and she collapses, helpless, in front of Supergirl.
Indigo reveals that it was she who activated Supergirl’s pod and sent both her pod and Fort Rozz to Earth. Moments later, though, she explodes into nothingness.
At CatCo, Winn tells Siobhan about his broken family, saying that he can understand how it feels when you’re let down by your parents, but it’s important to know that most people want to do the right thing. She throws herself at him, kissing him passionately, and then tells him that if he tells anyone about it, she’ll kill him.
In her office, Cat doesn’t believe the official story that the nuke was just a Russian Soyuz replenishing the ISS, and asks James how close they came today. He admits pretty close, and she goes home to have dinner with her son.
Cat leaves, and Kara tells James that it wasn’t really Lucy’s safety but her desire to have something special with James. She says to go ahead and tell Lucy.
Out on the patio, James goes to talk to Lucy, but she immediately breaks up with him, saying that she believes he loves Kara, and that’s why he told Kara the story about the camera. She tells him that Kara loves James, too, even if she can’t admit it yet.
At the DEO, Kara comes to talk to Henshaw, saying that she understands now that they need each other, personal feelings aside. When Henshaw wants to get down to business, Alex feels guilty and admits it was she and not Hank who killed Astra. She tells Kara she was afraid of losing her, and Kara comes to her, reluctantly giving her a hug. As Hank passes by them, Kara reaches out to hold his hand, too.
Elsewhere, Non has a spinning ball in his hand, which he places near a computer, rebuilding Indigo, telling her it’s time to do things his way.
