- For the titular character, see J'onn J'onzz.
- "Ancient Greeks had Hades. The Egyptians, Anubis. The Incas, Supay, the lord of the Underworld, god of death. Today, the villagers that live among the ruins of that empire believe that Supay has returned to live amongst them. But this creature is no devil, it is an alien fugitive, the Manhunter."
- —Hank Henshaw to his D.E.O. agents.
J’onn J’onzz reveals the details of meeting Kara and Alex’s father, Dr. Jeremiah Danvers, and assuming Hank Henshaw’s identity. Also, Kara debates trusting someone new with her secret identity and Siobhan plots against Kara.
At her apartment, sullen Kara Danvers watched a KPJT News report on her failed bank intervention from the morning, with everyone fleeting when she arrived. At CatCo Worldwide Media, Cat Grant held a meeting during which she complained about the citizens of National City's reluctance to forgive Supergirl, and the spiraling crime rate. Afterwards, she called for Kara though Winn had to remind her that Kara was out sick for the day. Winn then offered to man the phones, though he had to leave, as he was texted by Siobhan Smythe who asked him to meet her at Noonan's, leaving James to answer the phones.
At Noonan's, Siobhan tells Winn that she has been blacklisted; she can't even get an interview once she reveals who she is. She blames Kara, but Winn believes Siobhan will be back on her feet.
Meanwhile, at the D.E.O., Alex visits J’onn, who warns her to cut back on her visits given the near-certainty of a government investigation. J'onn's warning proves accurate; Alex is summoned to the main room to find a battery of soldiers have taken over headquarters. Their commander, Marine Colonel James Harper, is leading an investigation into J'onn's infiltration of the D.E.O. Lucy Lane has returned to the JAG Corps as a legal assistant in the investigation. The two take J'onn to an interrogation room that is protected with a stasis field so powerful that J'onn can't use his powers even if he wanted to. It also prevents Kara from listening in.
Inside the room, J'onn tells the two about what happened when he befriended Jeremiah Danvers ten years earlier in Peru. The real Hank Henshaw led a D.E.O. team to Peru to hunt down a dangerous alien fugitive they have been hunting for years. Jeremiah was against this; he thought they could learn something from the Manhunter. However, Hank wouldn't hear of it.
During the mission, a snake attacks Jeremiah, but J'onn saves him. That night, the two bonded and became friends. Jeremiah realized that J'onn is an alien refugee - just like his adopted daughter, Kara. J'onn explained that he had a family as well - including daughters - until they were killed on his home planet of Mars, leaving him the sole survivor. Jeremiah promises to help him and inform the D.E.O. that he wasn't a threat. Just then, Hank appears and shoots J'onn. Jeremiah comes to J'onn's defense, leading to a scuffle between Jeremiah and Hank. As they fight, Hank stabs Jeremiah, mortally wounding him. Jeremiah throws Hank over a cliff to his death. Before he dies, Jeremiah asks J'onn to watch over his daughters - prompting J'onn to assume Hank's identity.
Harper, who was close friends with Hank, doesn't believe J'onn means no harm, even when J'onn emphasizes that he helped protect Earth from numerous alien threats. Harper orders J'onn taken into custody over Alex and Kara's vociferous objections. Harper tells Alex she is next. Siobhan sneaks into CatCo Plaza and slips behind Kara's desk. She then sends a nasty email to Cat, on Kara's account.
Alex is polygraphed by Lucy and Jim. She explained how J'onn as Hank approached her to join the D.E.O. three years ago. After a night of drinking and clubbing led to her arrest, Hank visited her in jail. Hank told Alex that she was special just like Kara, and that she owed it to her father to be the person he knew she could be. When asked if she knew beforehand that J'onn was posing as Hank, Alex says "no" - and passes. However, Lucy doesn't believe her and places her under arrest. After Kara slips on Vasquez's earphones so she can listen in, she is stunned that Lucy and Jim are taking the two to Project Cadmus.
Kara tells James that J'onn and Alex have been taken into custody. James tells her that Project Cadmus is a genetic engineering facility where captured aliens are subjected to experiments. Superman is so opposed to it that he refuses to work with the government. This left Kara with no choice but to have James bring Lucy over to the apartment.
When Lucy arrived, Kara reveals that she is Supergirl. Lucy is still distrusting of aliens, and doesn't understand why they lie. This is when Kara explained to Lucy why she kept her powers a secret for so long. 12 years ago, while hanging out on the beach with some friends on her first day at school, she heard an explosion from a burning car. Her instincts kicked in, and she pulled a woman and her baby out of the car just as it exploded; Alex was injured by flying debris. Afterwards, Jeremiah gives Kara a pair of glasses lined with a little lead to suppress her X-ray vision. He tells her that the world doesn't need another hero, and she shouldn't use her powers lest she endanger people.
Years later, Kara starts her job as Cat's personal assistant. She tells Cat that she's not special, she just wants to be useful and is willing to meet Cat's demands for absolute loyalty and devotion. She tells Lucy that when you're an alien not living on your home world, you're willing to sacrifice everything just to fit in. She and James appeal to Lucy's better instincts.
Later that night, a military truck en route to Project Cadmus is intercepted by two motorcycles. The guards open fire on one of the cyclists, but the bullets bounce off him harmlessly. The other cyclist shoots out the truck's tires. While Harper is distracted, Alex crushes the device that maintains the stasis field, allowing J'onn to break free and overpower Harper. The cyclists turn out to be Kara and Lucy. While Kara disarms the guards, J'onn erases Harper's memory of having remembered meeting him. However, he gets a glimpse inside Harper's mind and discovers that Jeremiah is alive at Cadmus. Alex tells Kara that she will go with J'onn to find Cadmus. Kara offers to hide Alex in the Fortress of Solitude while she finds Jeremiah, but Alex insists that she has to be the one to find him.
Cat calls Siobhan in. Just as Siobhan thinks she's about to get her job back, Cat reveals that Winn analyzed the email Kara supposedly sent. Winn discovered that the typing pattern didn't match Kara at all - but it matched Siobhan. Cat brusquely orders Siobhan out, and threatens to call the police if she ever comes back again. Later on at the D.E.O., Vasquez informs Lucy that Harper has resigned - and at his insistence, Lucy has been named acting director. Upon being informed that a bank robbery is underway, Kara heads off to stop it. She doesn't know if National City will ever trust her, but Lucy says that if she can win her trust, she can win back the city.
Winn finds a severely drunk Siobhan on the roof of a nearby building. Siobhan is furious at Winn for turning on her, even as he tells her that criminal and manipulative behavior won't get her anywhere. Suddenly, one of Siobhan's spike heels breaks, causing her to lose her balance and stumble off the roof. She screams in terror, but just as she is about to fall to her death, the sound waves from her screams break her fall and blow a hole in the concrete, while an equally stunned Winn watches.
- J'onn is shown to like Chocos (a trademark-friendly version of Oreos), which is taken from the comics.
- Cat talks on the phone with a certain "Kate" who has an influential grandmother-in-law, referencing Catherine, Duchess of Cambridge and her grandmother-in-law, Queen Elizabeth II.
- The flashbacks featuring Kara were originally filmed for "" but were cut for time.
- Project Cadmus has a long history with Superman in the comics.
- At the end, Supergirl is called to a bank robbery at "10th & Shukert". This is a reference to episode writer Rachel Shukert.
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