As Clark and Lois drive down a country road, she asks him questions about his Kryptonian background and admits that she isn't used to learning that he's an alien. She insists that she's okay with that, and admits that she's glad they're out on a story with Kat around. However, Lois quickly realizes that Clark set it up to get her out of town, and he admits that Kat is covering an antihero protest. She mildly resents his overprotective attitude and insists she can protest herself. Two of their car tires blow out, and they only have one spare. There's no phone reception where they're at, and Clark fixes one tire. A young girl, Charlotte Cavanagh, runs over from a nearby produce stand, is happy that they're unharmed, and tells them there's a mechanic in Meeker Springs, two miles away. When Clark prepares to take Lois with him, she sarcastically insists that she'd better stay where she's at while Clark "rescues" her. Clark walks off as Lois and Charlotte watch.
A few hours later, Clark runs back and discovers that Lois, Charlotte, and the produce stand wagon have all disappeared. As Clark puts the spare tire back in the trunk, he scratches his hand and is surprised to discover that it's bleeding. A patrolman, Ellis, pulls up and Clark explains what happened, and that they had a minor argument. He describes Charlotte, but Ellis suspects that he's imagining things. Clark then finds a board with spikes driven through it, that was left on the road, and points out the wagon tracks. Ellis admits the tracks look fresh and agrees to help Clark search.
Charlotte has taken Lois into her town on the horse and buggy so that her father can take Lois to the train station in the next town. The girl explains that their entire congregation lives there after having moved from Idaho, and they're preparing for the harvest festival. Charlotte stops at her house and her mother Ruth greets Lois. She says that her husband will take Lois to the train station after supper, and warns that it's easy to get lost. Ruth invites Lois to stay for dinner and she reluctantly agrees. Charlotte goes to get her father, who says that she did great work and has saved them all.
Tess is throwing Alexander a 12th birthday party. He thanks her for the party and she says she has work to do. Outside, Tess talks to Dr. Christine Lamell, who says that she's looking for a cure but warns that Alexander's condition is irreversible and his body will soon give out. She wants Alexander taken to a facility for 24-hour observation, but Tess refuses and insists he be treated as a normal child. Lamell warns that Alexander will never be normal, and Tess notes that she worked for Lex and this is her change for redemption. Lamell agrees and Tess promises that she won't let Alexander become a monster. They hear a commotion from the next room and investigate. Alexander has collapsed, but not before drawing a familiar symbol in candle wax: the crest of the House of El.
Clark and Ellis continue their search and find an old cabin. Ellis insists there's an innocent explanation for everything, and says that Lois probably hitched a ride to Metropolis. Clark notices a water trough filled with blue crystals, and Ellis explains that a meteor shower hit the spring in 1989. It killed one local, but purified the water and made people remarkably healthy. Clark hears a bell tolling, and Ellis knocks him out.
Alexander is playing with Lex's chess pieces when Tess comes in to see him. He apologizes for ruining the party, but she says it isn't his fault. As she hugs him, Alexander steals the room key from her pocket. She asks how he knows the symbol, and reveals that she found other ones hidden in his closet. Alexander explains that it's the symbol of the "bad man," who comes into his dreams to hurt him. Tess insists that she'll protect him, but Alexander say she can't and snaps at her. When Tess turns away from him for a moment, he runs out the door and locks it behind him, trapping her.
Lois eats with the Cavanaghs, and Mr. Cavanagh talks about staying on the righteous path. She tries to get him to take her to the train, but he insists that she stay to finish dinner and Ruth says that it's bad luck to leave early. Mr. Cavanagh explains that they hold the harvest to celebrate a sign, a fire that came from the heavens and destroyed much of the town and killed their daughter, Esther, when she rang the town bell to warn the townsfolk. Before that, they suffered years bad crops. Ever since, they've had bountiful harvests, and they believe that Esther's death was responsible. Mr. Cavanagh explains that every year since then, they've offered the Lord a sacrifice and have been rewarded.
Once the Cavanaghs go to put away the dishes, Lois tells Charlotte that she has to leave. Charlotte tells her that she won't be allowed to leave, and this was Lois' last supper. She runs outside but finds the villagers waiting to take her prisoner.
Clark wakes up in the Cavanagh house and finds himself with Lois, trapped in a room with the townsfolk watching outside. She explains what's happened and Clark tells her that the townsfolk have been drinking blue-kryptonite-tainted water, and they negate his powers when they're near him. Lois realizes that she saved his life when she pulled the blue kryptonite dagger from his chest, and Clark thanks her. They find a cellar door but discover it's locked. However, Lois goes to work with a bobby pin and tells Clark to change into local garb so he'll blend in when they escape.
Tess' people track Alexander to the Kent barn. She goes there and Alexander explains that he remembers everything he did when he met with Clark, based on the memories of his predecessor. The boy grows angry at Clark for all of his betrayals, and Tess tells him that he can choose to be good. However, Alexander "remembers" Clark refusing to trust him, and Tess insists that Lex used them both. She offers to help him, but Alexander accuses her of doing it for selfish reasons and clinging to powerful men. Tess slaps him and then apologizes, calling him Alexander. He warns that she can't even save herself, and tells her to call him Lex.
Clark and Lois slip out through the cellar and try to blend in with the crowds. A village woman notices Lois' painted fingernails and realizes that she's an outsider, and sounds the alarm. Lois punches her and they try to run out of town, but Cavanagh cuts them off. and the villagers recapture them. When Clark refuses to let them hurt Lois, Cavanagh stabs him in the chest and leaves him to die in the road.
At the town square, Lois has been placed beneath the warning bell, which is filled with the blue flame. Cavanagh explains that they killed a woman during harvest every year for the last 20 years, and Lois says that Esther would be ashamed of what he's done in her name. Some of the crowd responds to her words, but Mr. Cavanagh warns that if they don't sacrifice a non-believer, then one of theirs will be chosen. They rally behind him, and Cavanagh tells Lois that the Lord forgives her.
Ellis and the village woman bury Clark and go back to the ceremony. Once they're gone, Clark's powers are restored and he digs his way out of the ground.
Cavanagh begins the ceremony and prepares to drop the blue flame on Lois. Clark grabs a shotgun and tries to stop them, but Cavanagh releases the flame. Clark leaps in and takes the burst on his back. Cavanagh backs away, insisting that it's a trick, but Ellis and the others think that it's a sign. They back away in horror, and Clark's wounds heal as his powers are restored. Lois leaps in and tells them to keep moving back because they're not worthy. Cavanagh picks up the gun but Lois tells him to surrender and respect Clark as a messenger sent from the heavens. Clark then superspeeds away with Lois, leaving the townsfolk in awe.
Tess is considering the cure that Dr. Lamell has provided, using research from Peter Dinsmore's attempts to stop his cloned daughter from aging. Dr. Lamell admits that's all there is for now. Tess considers the small vial of serum, and then throws it into the fire. She tells Lamell to destroy all of her research. Alexander will be locked up and left to die in six weeks, and Tess tells Lamell that the boy isn't just a clone: he is Lex Luthor.
Lois come to see Clark at the barn and shows him how their story about backwoods cultists bumped Kat's story on the antihero rally. When Clark wonders how they could have gone down such a dark path, Lois says that it may be time for him to emerge from the shadows and become a symbol of hope. She's sure that if they knew him like she did, they'd respect the real Clark Kent. Clark apologizes for being overprotective, and admits that she held her own when he didn't have his powers. Clark gives her Dr. Swann's journal of Kryptonian lore and they kiss, and end up in bed.
Locked up somewhere, Alexander sketches more El symbols and then cuts off his hair. Bald, he looks into the mirror and smiles.
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