After Livewire seemingly breaks out of prison, Supergirl is intent on recapturing her. After training Mon-El, Supergirl takes him with her when she sees Livewire attack the NCPD but things go awry when Mon-El puts Supergirl before the citizens of National City. Meanwhile, James decides to come clean with Kara and M’Gann, has a psychic attack and collapses into a coma.

A new villain comes to National City, putting Supergirl on high alert. Meanwhile, Winn’s girlfriend, Lyra, gets Winn in trouble with the law. Maggie attempts to help Winn but old loyalties get in the way. The Music Meister attacks Supergirl.

The crossover continues on The Flash S03E17 Duet (II).

Kara investigates a secretive new group whose leader, Thomas Coville, has a mysterious connection to Supergirl. Meanwhile, Samantha feels like she's letting Ruby down, and J'onn confesses an old secret.

Supergirl is stunned to discover that a part of Krypton survived. Meanwhile, Alex is attacked while out with Ruby, and Lena considers how far she will go to keep Reign contained.

James falls in deeper with the Children of Liberty in his efforts to meet Agent Liberty. Meanwhile, 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.

Supergirl, Alex, and Brainiac thwart an alien attack while William investigates Kara. J'onn J'onzz and Kelly use Obsidian tech to solve a problem.

Supergirl finally learns the truth about Lena while tangling with Leviathan. J'onn J'onn makes a discovery about his brother's whereabouts.

As Supergirl tries to thwart a Toyman copycat, Winn Schott returns from the future.