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 the stakes with Lex are raised higher than ever before, Lena must decide how far she is willing to go to stop her brother. Meanwhile, Supergirl and the team are faced with a challenge unlike anything they've ever dealt with before and it brings Alex to her breaking point.
Supergirl makes a new ally. Lena and Lex battle for control of Luthor Corp.
Supergirl finds an opportunity to escape from the Phantom Zone but it comes with some dangerous strings attached. Meanwhile, Lena joins the Super Friends on a mission but finds she disagrees with their plan of action against the Phantoms and wonders if she is truly ready to be a part of the team.
Nia and Brainy attempt to save Supergirl from the Phantom Zone by time traveling back to Kara's home in 2009. While determined to secure the item needed to help Supergirl, Brainy is worried about keeping a low profile so as not to alter the future timeline. However, when their ship crashes upon arrival, a young Kara Danvers is the first on the scene. Meanwhile, a young reporter named Cat Grant sets her sights on Midvale as she suspects there is a big story in the small town.
Part two of the flashback episodes pick up where things left off - Young Kara experiences kryptonite for the first time, Nia and Brainy are trapped by invading aliens, and a young Cat Grant may be the reason Supergirl never gets out of the Phantom Zone.
As the Super Friends brave the Phantom Zone to bring Supergirl home, each member of the team is confronted by visions of their worst fear.