“What Lies Beneath” is episode one of season two of Superman and Lois.
At the end of the season one finale, “Last Sons of Krypton”, a pod crashed on the farm, inside which was John Henry’s daughter, Natalie. Natalie saw Lois – who was her mother in her own universe- and called out to her, starting to rush over.
John Henry tells Natalie Lois isn’t her mother. She’s still gone. He leads her away to explain and Clark tells Lois she has to say something. Lois turns and heads for the house as John Henry and Natalie drive off in the RV.
Three months later and Clark is looking for a bottle of Lana’s favourite wine. Lois suggests he swing by the shop to get one. She’s reviewing job applications for the Gazette which she now co-owns. Jordan has overdone the cologne – Sarah is back after a month. Clark mentions it’s Natalie’s first day at school; perhaps Lois could call her. Lois says Natalie still won’t talk to her. When she leaves the room, Jonathan asks how long she’s going to be like this, as she’s clearly off. Clark doesn’t know.
In Smallville, Kyle is complaining to Lana about someone selling Superman stuff. A bus arrives and Sarah gets off; she was at camp as a counsellor.
Chrissy is interviewing someone at the Gazette when Lois arrives and shows him the door. Lois says if the rest of today’s interviews are like that, cancel them. Chrissy says Lois hasn’t liked a single person. They need someone and will gave to compromise. Lois reluctantly agrees.
Lana has campaign t-shirts for Daniel Hart, who is going to run for mayor. Jordan knocks and he overhears them talking inside. Sarah doesn’t seem that enthused to see him, though she agrees to meet later.
At training, Jonathan isn’t pleased he’s not been called for the right sort of plays, and is complaining when he, Clark and Jonathan’s girlfriend, Candice, arrive home. Clark doesn’t get anywhere talking to Jonathan but Candice quickly does. He throws his hands in the air, then hears a North Korean sub having problems and excuses himself. Superman arrives over the sub, which is sinking rapidly, then gets overwhelmed by sounds and images and falls into the water. He’s able to recover and get to the submarine just in time, carrying it to shore.
In Metropolis, John Henry is schooling Natalie on her fake identity. She’s going to her old school and warns her that her former best friends are not that here. He doesn’t want to attract unwanted attention. Natalie makes a comment about him flying around the world in a steel warsuit with Superman.
Lois arrives home to find Jonathan and Candice about to get far more physical than Lois would like. She is not happy.
At the DoD, what is presumably Sam’s replacement, General Anderson, is on the phone. He wants to talk to Superman and has an ELT. Superman arrives and is told that rescuing a North Korean nuclear sub isn’t playing well. Couldn’t he have dropped it off on American soil? Superman doesn’t get involved in politics. Anderson wants Superman’s firm commitment that he will put American interests first. Or their working relationship will have to change. The best Superman can do is continue to do everything he can to help the DoD. Then he hears Lois calling for help.
Which is not an emergency, but help with telling Jonathan off. Jonathan is sent to his room; he goes gladly. Lois explains what she found and she isn’t happy that Clark left their 15-year-old son at home with his girlfriend. Clark would never have done anything at Jonathan’s age. Lois comments Jonathan clearly takes after his mother. And she’s concerned what Jordan might be doing. The whole thing ends up with Clark going to Lana’s by himself.
Much of the episode is about relationships. Natalie is struggling being in a new universe, Sarah’s feelings for Jordan may have changed, Kyle is a bit jealous about Lana working with the mayoral candidate and something is clearly up with Lois. It’s not until close to the end, and at the end, that anything new really happens. Other than Clark’s strange experience when he went for the sub. Which is not the last time that happens.