The episode opens with Lena Luthor lying in bed inside a Daxamite ship. Rhea says that she saved her from Supergirl and that Lena is destined for greater things. Rhea says that Lena belongs by her side, ruling a new Earth.
The camera then cuts to the Daxamite fleet blasting the heck out of National City. Daxamite shock troops teleport to the ground and begin attacking National City's citizens...including the police department. Maggie shoots a few down and then calls Alex for help, but the DEO's headquarters quickly falls under attack too. As DEO agents fall to Daxam's forces, Winn takes cover and hides within the DEO base while Alex jumps off the balcony, just in time to get rescued by Supergirl. Supergirl says they need to hide as Rhea declares National City to be "New Daxam."
Back on the Daxamite ship, Rhea talks to Mon-El about her invasions. She says she plans on rebuilding Daxam on Earth, enslaving humans in the process. Mon-El says that humanity (and Supergirl) won't fall so easily, but Rhea has plans to take care of both, by marrying Mon-El off to Lena Luthor.
Winn, Alex, and Supergirl set up a temporary DEO base inside the Alien Bar. Martian Manhunter is still down from whatever Rhea did to him last episode. James shows up at the bar and says that the Daxamites have quickly taken over. Supergirl also can't get a hold of Superman either. Maggie pops into the bar too, but things still look pretty grim. Suddenly, Lillian Luthor arrives at the bar (how did EVERYONE know to head there) and offers to help.
Lillian says that she needs Supergirl's help and they clearly need her help. After all, Lillian is an expert of ridding the Earth from an alien threat. Lillian also points out that the Daxamite ship has a kryptonite cannon, so Supergirl can't get aboard. She says that she just wants to save Lena, but Alex and Supergirl both reject her offer. Lillian does leave a burner cell phone in case Supergirl changes her mind.
The president of the US calls Rhea and demands that she call off her invasion. When Rhea refuses, the president reveals that she's on Air Force One and heading towards National City. As the situation escalates, Cat Grant steps in (she's advising the president) and tries to get them to talk peace. However, Rhea shuts off the line and shoots down Air Force One. As the plane plummets to Earth, Cat flies out the side, but she's quickly saved by Supergirl. The rest of Air Force isn't as lucky. Supergirl fears that the president is dead, but the president emerges from debris in her Durlan form.
Cat and Supergirl bring the president into the makeshift DEO headquarters. Cat explains that she "hitched a ride" with the president when the invasion broke out and casually mentions that the president is an alien. The president explains that she's a refugee from an alien world - which explains why she's a big believer in refugree rights. She orders Alex to use the DEO's positron laser to shoot down the Daxamite ship, over Supergirl's objections.
Rhea brings Mon-El and Lena into her throne room and says that they'll go through with the wedding or she'll blow up the Luthor Foundation Children's Hospital. Rhea also wants them to produce an heir, which she can make using their genetic samples.
Alex tells Supergirl that she's going through with the president's plan, even though Supergirl says its wrong. Supergirl storms outside and has a talk with Cat Grant. Supergirl says that her best friend and boyfriend are both trapped in the ship and that her life would be destroyed if they destroyed that ship. Supergirl says she's just being selfish, but Cat says that she's just being human. Cat Grant tells Supergirl that she wasn't happy in National City and eventually discovered that it's not about what you do, it's about who you love. Cat's speech inspires Supergirl to take action and save her friends. And Supergirl's first step is to find Lillian Luthor.
Supergirl brings Lillian back to the bar with Hank Henshaw. Lillian's plan is to use Superman's Phantom Zone projector to transport Henshaw to the Daxamite ship, where he can then bring everyone else aboard. When Supergirl saves Lena and Mon-El, Alex can then blow up the ship. Cat volunteers (with Winn) to create a distraction. Before they leave, Winn plants something on Henshaw, presumably to keep him in line.
Supergirl, Henshaw, and Lillian successfully enter the Phantom Zone, as Rhea presides over Lena and Mon-El's wedding ceremony. Meanwhile, Cat goes back to her office (disgusted at what James has done to the place) and sets up a broadcast.
Supergirl's team transports into the Daxamite ship and start fighting their way through the ship. Right before Rhea finishes the ceremony, Cat's broadcast interrupts them. She urges National City to "resist," and convinces the city to spontaneously start fighting back again.
Henshaw successfully hacks into the Daxamite system. He finds Lena, just as Lena and Mon-El stage their own breakout attempt. Meanwhile, Alex gets the cannon ready to fire just as Supergirl finds Mon-El and Lena on the ship. Lillian grabs Lena and transports away, leaving Supergirl and Mon-El behind. Lillian then calls Alex and tells her to fire the cannon. Alex, thinking that Supergirl is with Lillian, charges up the big gun.
Lena tells her mother to turn the teleporter back on, but Supergirl is one step ahead of her. Turns out that Winn bugged Henshaw so that Supergirl could remote control him. Supergirl tells Mon-El that he needs to teleport away, but that she's going to stay behind and give his mother the chance to surrender gracefully.
Daxamite soldiers teleport into CatCo to kill Cat, but Guardian shows up to rescue them. After Guardian takes care of the Daxamites, Cat thanks him and reveals that she knows James Olsen is behind the helmet.
Mon-El teleports into the Fortress of Solitude and gets in touch with Alex. He tries to wave Alex off, but the president orders Alex to shoot the Daxamite ship down.
Supergirl tries to get Rhea to surrender, but she's totally unmoved. Rhea reveals that she has another trick up her sleeve, as a heat vision blast destroys the DEO's cannon. Supergirl turns around and gets punched in the face by Rhea's secret weapon: the Man of Steel himself, Superman.