“Wake Up” is episode seven of season three of Supergirl.
A sub is examining the waterfront for damage caused during the attack in “Girl of Steel”. They discover the alien ship that was uncovered, and it fires something at them.
Sam is at home thinking. She tells Ruby to go to Tess’s for dinner, as she has to go back to work.
Winn finds M’yrnn looking for the bathroom. He asks permission to leave. Winn finds J’onn and says that J’onn’s father asked for permission to use the bathroom, as if he’s a prisoner or something. J’onn says he was one for 300 years. Winn thinks J’onn should take his father out into the non-DEO world.
Supergirl flies in; Winn had called her. He explains that something strange was found in the bedrock at the waterfront, which managed to make it to the surface. Winn uses another way of scanning. The ship has been underneath the city for 12,000 years. And the metal isn’t on the periodic table.
In the city, Supergirl is going to drill down but J’onn has a better idea. He transports her and Winn to the ship. They find some kind of stasis tubes, and one is empty. The former occupant appears and shoots at Supergirl. It’s Mon-El.
Alex arrives at the DEO; they’re trying to work out how Mon-El is still breathing. Winn asks what language Mon-El was speaking. Saturnian. He didn’t fire on the sub; it was the ship’s defence systems. In the other chambers are passengers. They aren’t dangerous. He says he’s hazy from hypersleep. Kara shoos the others out. She mentions it being 7 months; his reaction suggests it has been longer for him.
Sam hasn’t gone to work. She gone to see her adoptive mother, Patricia, who kicked her out when she became pregnant with Ruby, as if you have a child, you are not a kid. Sam wants to know if she ever did anything strange when young. Apparently not. Sam wants to know about her birth mother, but thinks it was pointless coming. But mentions how she was shot in “Damage” and didn’t even feel it when the bullet flattened on her skin. Patricia tells Sam to come with her.
In an outbuilding is some kind of craft. Patricia didn’t adopt Sam; she found her in the craft and took her home. She’d planned to tell Sam when she turned 18, but Sam was already gone and Patricia thought that maybe she was better off not knowing. Sam touches the craft which activates and a crystal is extruded.
Sam decides to head off to find out more about herself. Some of it can already be guessed. M’yrnn doesn’t think he’s a prisoner of the DEO; he thinks J’onn is, as he has nothing outside of work. Mon-El is keeping secrets, as can be guessed.