At the start of the episode, we see a teenage Clark Kent, following his sunstone through the frozen landscape where we last saw his adult self. The sunstone stops guiding him and, frustrated, he throws it down into the snow. A Fortress erupts around him, blowing him clear of its path. He heat-visions his way out of a snowbank and makes his way to the mouth of the Fortress, where the sunstone now floats over a dais. He grabs it, and after examining the icy dais, affixes the Sunstone to it, bringing Jor-El to “life.” He explains to the teen that he is Jor-El, and he is the boy’s biological father. He tells Clark that he can learn lessons about who he is and why he was sent to Earth in the Fortress. Jor-El explains his powers, and we see a Superman: The Movie-style montage of Clark learning to use his powers, evolving from the teen into Tyler Hoechlin’s adult version, and eventually taking flight.
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After telling Jor-El he is ready, Jor-El tells him that he needs to reconnect with the world and learn why he wants to help humanity.
At the Kent farm, Clark arrives home to find Martha sweeping the porch. They embrace, and she asks if he found what he was looking for. He tells her he did, and gives her a quick download as to what happened at the Fortress. He tells her that he knows why he can do things, and why he was sent to Earth. WE see him replacing the sunstone, and looking around the Kent household, telling her that before he can leave town he needs to see Lana.
Heading into town, he sees her at a movie theater, but before he can approach her, he sees her embrace Kyle, then zooms his telescopic vision in on her finger, where there’s an engagement ring. Back at home, Martha consoles him, then opens a suitcase. In it, she has packed up some of his things, saying that she had a dream of him flying. She gives him his first costume, which she tells him she made.
Clark tries to apologize for leaving after Jonathan’s death, but Martha tells him that she knows it’s what he needed to do then, and this is what he needs to do now.
In Metropolis, Clark is apartment hunting when he hears a car out of control, and changes into his costume for the first time. This brings us back to that moment from the pilot, when he saves the boy from being crushed by a falling car. After saving the kid, Clark rushes back and changes back into his civilian clothes in a phone booth. He looks up after a brief encounter with a passerby, and sees the Daily Planet building.
Inside the Planet, Perry White blows off Clark’s resume, but hires him when he agrees to work cheap and do whatever he’s asked. Cut to the scene from the pilot, where he first meets Lois and is immediately smitten.
Lois is frustrated by the fact that since Superman arrived, systemic issues have taken a back seat to Superman’s more flamboyant exploits. Clark asks her how he can help, and cut to the two working together on the case. She walks him through being a reporter in a big city, and they have a montage of investigating some neo-Nazis attacking minority-owned businesses. Late at night, as they work together on the story, Clark compliments Lois’s reporting skills, then starts to excuse himself but instead ends up in a conversation where he is cornered into almost admitting feelings for Lois. The next morning, she isn’t at work when he arrives, and he flies off to stand in between her and the neo-Nazi, now in costume as Atoman and about to kill Lois with a flamethrower. Superman blows the flamethrower out, but the villain throws a pair of grenades into the crowd around him, assuming Superman can’t stop both. He does, but is blown through a window by one. Lois knocks out Atoman with a taser, then has her first meeting with Superman, where she decides on his name.
Cut to Lois with Superman, doing his first on-camera interview for The Daily Planet’s video service. She asks what he stands for, and he gives her truth, justice, and she goes with the American way, trying to get him to admit details about his private life. After her mic malfunctions, a producer pulls Lois aside and tells her that she thinks Superman has a crush on Lois. She tells her that she isn’t interested in Superman, and that she’s in love with Clark. The producer notices Superman looking at them, and asks about his super-hearing. Lois goes back to the interview, which then cuts to Lois about to meet Martha for the first time. She has set up a small get-together to welcome Lois, and afterward tells Clark that she’s wonderful. Clark tells Martha that he brought her to Smallville to tell her who he really is, and as they hug, Lois comes in to see them. He takes her outside and flies for her, then cut to the pair of them in the newsroom, kissing, and again to him proposing outside the Fortress door, and to their wedding.
He tells Lois that he realizes now why he kept his secret from everyone — it’s so that they can have a life together.
Later, he tells Jor-El about the marriage, and Jor-El screams at Clark to get out. Then Clark wakes up in a hotel room, and looks around, confused.
As Clark is wondering what day it is, Lois comes out to tell him she’s pregnant. As Clark begins to grapple with the shifting reality around him, Lois continues in her script. At the doctor’s office, Lois learns she is going to have twins, and he sees a shadow flickering out of view. He walks toward it, but Lois keeps talking to him as if he were still talking to her in his flashback. Outside, he sees his half-brother, who has infiltrated Clark’s flashbacks to learn that Superman has a family and exploit it to try and force him to surrender.
Tal Rho tells Superman that he will tell the world his secret and put his kids in danger if Superman won’t surrender. After Jor-El arrives to discourage him from listening to Rho, Rho destroys the sunstone, “killing” Jor-El, and knocks Superman out, then leaves.
Back in Smallville, Lois is talking to Lana and Kyle. Kyle is worried that when the truth finally comes out, he’ll be one of the people the town blames for everything that happened.
In their living room, the boys are talking to Sarah. She’s frustrated by all the lies going on, and thanks the boys for being honest with her. They’re both guilty over not sharing everything with her, and she asks for a moment alone with Jordan. He starts to apologize for not telling her everything that was going on with her dad, but she kisses him and tells him that she doesn’t want to be just friends anymore. Before Lois and the boys leave Lana and Kyle’s house, Kyle stops her to apologize about the way he’s treated her since she got to town, telling her that she’s good people, and he’s glad she’s part of Smallville.
Rho drops down from the sky in front of Lois and the boys as they arrive home.
Lois tells him to leave, and he threatens the kids. After a brief squabble, he tells Lois that he’ll let the kids live long enough to watch Lois die. As he charges up heat vision, though, Superman drops out of the sky, and tells Rho that he will do whatever he wants to save his family.
Clark tells Lois “he was right” before being flown off with Morgan to the Evil Fortress in the desert, where we get a flashback to teenage Morgan Edge creating his own fortress in the desert by planting his sunstone and calling on his father, who berates him becuase by 1987, he didn’t yet have the Eradicator. He says that he will train him, so that he will have no weakness, and begins torturing him with red sunlight.
In the present day, the Rhos are ready to begin their plot, with the Eradicator in their possession. As they start to “eradicate” Clark, Lois calls John Henry, telling him that “it’s happening, just like you said it would.”