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 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.

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 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.

Supergirl intervenes when a building in the Heights that was set aside for low income housing is suddenly at risk to be sold to a major corporation. Supergirl recruits Orlando to help her win over the city, but things go awry when Nyxly shows up. Meanwhile, Nia trains with her mother.

Kelly is horrified when the Ormfell building implodes, injuring many in the community, including Joey. However, her horror quickly turns to frustration when she realizes that the hospital is overwhelmed, people are getting sicker, and no one is coming to help - including Supergirl who is busy fighting Nyxly. Knowing that she can make a difference, Kelly embraces her power and fully steps into her role as Guardian. Joined by Supergirl, Alex, Diggle and team, Guardian leads the way to restoring justice to the fallen community.

Lena is uncertain about using her magical abilities to help Supergirl retrieve the second totem from Nyxly. William struggles to write a story on the Super Friends that makes both the heroes and Andrea happy. Meanwhile, Kelly is thrilled Esme has found a new home, but things go awry and the little girl's future is put in danger.

Kara lands her dream story for Catco but when the city is suddenly attacked by a nightmare monster at the same time as her interview, she is forced to take a serious look at her life and decide if she can continue to live as both Kara and Supergirl. As Dreamer takes the lead on the search for the Dream Totem, which can vanquish they nightmare monster in National City, she realizes she needs to ask her sister Maeve for help.