Kara welcomes a new cub reporter to CatCo; James and Lena argue about James' impending indictment for acting as the vigilante Guardian; Alex and Brainy struggle to get in sync at the DEO.
A shocking revelation causes chaos in National City; Supergirl sets out to capture Mercy Graves, while Alex takes control at the DEO; Kara decides to write an investigative story on Mercy and looks to Lena for information; Brainy meets Nia.
Through a series of incidents, and input from his anti-alien father, Ben Lockwood slowly transforms from a mild-mannered professor into the villainous Agent Liberty.
When Supergirl needs help, Alex asks Lena and Brainiac to team up; J'onn questions his decision to quit the DEO, but after running into Manchester Black, he realizes there are a lot of ways to help his fellow aliens.
Col. Haley makes a surprising decision regarding Supergirl; Kara writes a series of articles highlighting aliens in National City in the hope of making humans less fearful of them; unfortunately, the article puts some of the aliens in harm's way.
As everyone gathers for Thanksgiving, Kara is feeling down after her televised debate with Ben Lockwood; James and Lena argue about the best way to handle the Children of Liberty.
James falls in deeper with the Children of Liberty in his efforts to meet Agent Liberty; Supergirl and Manchester Black follow a lead on Agent Liberty's location, but things take a dark turn; Lena kicks off her first set of trials.
Nia has a powerful dream about Agent Liberty but refuses to look at it as a prophetic dream; Kara and Brainy try to persuade Nia to embrace her destiny; Manchester Black pays Ben Lockwood a menacing visit.
Supergirl, The Flash, Green Arrow and Superman engage in the battle of their lives.
When Supergirl angers Col. Haley by refusing to be told what to do, Haley refocuses her energy on learning Supergirl's true identity; Brainiac-5 encourages Nia to embrace her powers.
Kara joins Nia on a trip to Nia's hometown to visit her family during the town's annual Harvest Festival; Alex deals with a street drug that is turning people violent and giving them temporary superpowers.
J'onn welcomes clients to his new office; Kara teams up with J'onn on an assignment, which unfortunately ends up tying directly into Alex's current investigation involving the villain Menagerie; Nia invites Brainy to her Valentine's Day party.
Manchester Black breaks out of prison with the help of his new team, the Elite; Supergirl tries to apprehend Black and his team while dealing with a shocking new development involving Ben Lockwood.
When Lockwood organizes a rally, the aliens decide to peacefully protest; Brainiac and J'onn join the alien march, while Supergirl and Dreamer patrol to keep everyone safe; Hayley assigns Alex a job that clashes with her beliefs.
Secretly furloughed from prison due to failing health, Lex Luthor visits his sister to seek her help; Lena is suspicious of Lex's motives, but when she's faced with a life and death situation, she must decide how she truly feels about her brother.
In the wake of Lex Luthor's return, flashbacks show what he's been doing for the last two years and how his secret machinations and plans have affected Supergirl and Lena.
Supergirl must deal with the destructive aftermath of Lex's nefarious plans; shocked at what Lex has created, Supergirl faces her biggest challenge yet.
Kara and Lena head to Stryker's Island to search for clues on how to defeat Lex; Kara tries to befriend a prisoner who may have insight into what Lex was doing; Kelly encourages James to talk to someone about his PTSD.
Kara doggedly works as a reporter to clear Supergirl's name; Dreamer picks up the slack as National City's protector, which leads to a showdown with Ben Lockwood; James takes drastic measures to relieve his PTSD.
Kara and Lena head to Kaznia to hunt down Lex; Eve Tessmacher sets a trap that could ultimately reveal that Kara is Supergirl; Alex gets a long-awaited phone call; James practices using his powers; Ben Lockwood takes a dangerous stand inside the DEO.
Kara comes face to face with Red Daughter and the two engage in an epic battle; Lena turns to an unlikely source for help; Alex realizes she's missing parts of her memory; Brainy, Nia and J'onn set out to track down aliens who have been abducted.