Alex is thrown off when she has a dream of her and Kara when they were younger falling off a cliff.
Kelly assures Alex that this is just a result of her adoption falling through, but Alex knows the last time she had such ominous dreams, Kara was in danger.
Sure enough, Supergirl is in danger. She's been kidnapped by the President's goons for threatening to leak incriminating information.
Supergirl makes an escape but comes face-to-face with the Red Daughter who weakens her with kryptonite.
As she's tied up, Supergirl gets to know the Red Daughter and realizes she's been completely brainwashed by Lex Luthor.
She overpowers the kryptonite and escapes to J'onn.
When Brainy informs her that Alex is working to track down the Red Daughter, she sneaks into the DEO and offers to help.
Colonel Haley walks in on Alex working with Supergirl and isn't pleased, but once she realizes President Baker has aligned himself with Lex Luthor, she comes around.
Alex locates the Red Daughter's address and Supergirl checks out the loft only to realize the Red Daughter has been spying on her.
Alex arrives on the scene and is confused about why the apartment looks just like Kara's.
She gets a call from her mother, Eliza, who informs her that Kara is at her house.
Supergirl rushes off to her mom's house knowing it's the Red Daughter.
A fight ensues between the two of them and the Red Daughter overpowers Supergirl with her evolved powers.
Alex arrives just as the Red Daughter is beating Supergirl and her memories of Kara being Supergirl begin flooding in.
The Red Daughter departs after ensuring Supergirl's heart has stopped, but Alex begs Kara to pull sunlight from the ground.
As she cries over her sister's body begging her not to leave, Supergirl draws sunlight and awakens.
Meanwhile, Brainy, J'onn and Dreamer team up to find the missing aliens.
The hope is that is the aliens will lead them to Lex Luthor.
J'onn asks them to hold off on shape-shifting or using an image inducer to sneak in because there's a high probability they'll get caught.
Brainy, who is consumed by his romantic feelings for Nia and wants to tell her, ignores J'onn's warning and agrees to use the image inducer to sneak them in.
He's convincing enough as Ben Lockwood, but a dog starts barking thus revealing them to be aliens.
They're both locked up and the guards begin rebooting Brainy until he's no longer the lovable DEO employee but rather, more crass and cold like his ancestors.
Brainy leaves Dreamer locked up and leaves behind J'onn explaining that they'll both go through the Transmatter where they'll be able to Astral Project their findings.
Otherwise, he doesn't seem too concerned if they don't survive.
Lena approaches Ben Lockwood to confront him about working with Lex Luthor.
Lockwood assures her all of his success is earned through hard work, but Lena assures him he's just a puppet in Lex's master plan.
She notices Lockwood's condition is deteriorating after taking the untested Harun-El serum, but the again tells her he's fine.
Lena and James follow Lockwood to Otis Graves' lair where Lockwood confronts him about Luthor.
He's shocked to find out that Lena was right.
Graves also tells him Luthor's whole plan is to convince Kaznia to attack America, turn on them, and then save America and be hailed as the hero he's always dreamt of being.
Lockwood kills Graves and runs off.
James begins showing signs of deterioration so Lena takes him to her mother, Lilian's cell.
Lena poisoned Lilian to convince her to work on a way to extract the serum.
She knows Lilian isn't lying because she unleashed a truth seeker on her.
As Alex and Lena figure out what Lex wanted with the Claymore Technology, President Baker addresses the nation with a special report.
Kaznia attacked America, but Lex Luthor thwarted it and neutralized Supergirl.