Diving back into reporting, Kara welcomes a new cub reporter to CatCo. Meanwhile, James and Lena argue about James’ impending indictment for acting as the vigilante Guardian, while Alex and Brainy struggle to get in sync at the DEO. Supergirl is called into action when remnants of the anti-alien terrorist organization Cadmus try to assassinate pro-alien leaders, but their endgame turns out to be much more sinister than she expected. J’onn relishes his peaceful new life, but an outing with an old friend causes him concern.

A shocking revelation causes chaos in National City. Supergirl sets out to capture Mercy Graves, while Alex takes control at the DEO. Back at CatCo, Kara decides to write an investigative story on Mercy and asks Lena if she can interview her as Mercy has ties to the Luthors. Meanwhile, Brainy meets Nia and the two end up in a precarious situation.

Nia has a powerful dream about Agent Liberty but refuses to look at it as a prophetic dream and pushes it aside. After noticing something is bothering Nia, Kara enlists Brainy's help, and the two try to persuade Nia to embrace her destiny. Meanwhile, Manchester Black pays Ben Lockwood a menacing visit.

Kara joins Nia on a trip to Nia's hometown to visit her family during the town's annual Harvest Festival. While home, Nia's mother encourages her daughter to embrace her destiny. Meanwhile, Alex deals with a street drug that is turning people violent and giving them temporary superpowers.

Manchester Black breaks out of prison with the help of his new team, The Elite, who are set on punishing the anti-alien forces. Supergirl pulls double duty as she tries to apprehend Manchester Black and his team as well as deal with a shocking new development with Ben Lockwood.

Between Ben Lockwood’s new push to stir up the anti-alien movement and the Elite’s desire to target Lockwood and his minions, Supergirl is concerned about the safety of the American people – both human and alien. 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. Meanwhile, James picks up his camera again to cover the march for CatCo, and Hayley assigns Alex a job that clashes with her beliefs. When The Elite and Ben Lockwood stir up trouble at the rally, Supergirl is forced to take a stand.

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. At the prison, Kara tries to befriend a nosy prisoner, Steve, who may have insight into what Lex was doing, while Lena studies an array of puzzles Lex left behind in the hopes of discovering his whereabouts. While there, a prison riot breaks out and Kara must find a way to stop the prisoners without revealing her secret identity as Supergirl. Meanwhile, Kelly encourages James to talk to someone for his PTSD, and Alex faces off against Ben Lockwood after he storms the DEO and acquires some powerful weapons to hunt Supergirl.

As Brainiac lays close to death after trying to stop Lex, Supergirl and team soar in to save him, engaging in an epic battle with Gamemnae. After beating Leviathan, Supergirl turns her attention to Lex who has used the Obsidian platform to brainwash half the world to love him and follow him at all costs, no matter what horrible things he does. Knowing how dangerous this makes her brother, Lena enlists the entire team – Alex, J’onn , Dreamer, Kelly and Brainiac – to help, but Supergirl realizes that the only way to truly stop Lex is to sacrifice herself.

As Supergirl and Zor-El make their return to National City, they are determined to keep the Phantom Zone behind them and enjoy being superheroes together. Unfortunately, their overzealous efforts backfire, creating a whole new threat to National City.