Lionel Luthor and the Luthor family war
44 episodes of Smallville carry this thread, 1d 20h in all — 19 of them are in The Essentials.
Arc membership is derived from each episode's own summary text, gated to the seasons the sources place each arc in. It shows where a thread is foregrounded, not every episode it touches.
In airing order

In rural Kansas, teenage Clark Kent saves the life of Lex Luthor after a car accident.

An old Kent family friend, who suffers from uncontrollably violent convulsions after working for Luthor Corp., shows up at the farm after accidentally killing a man in Metropolis. Meanwhile, when Clark's parents head to the city for a romantic getaway, the teen decides to host a party that soon gets out of hand.

A teen whose family lives and works in the Luthor mansion has a crush on Lex, and her jealousy of the tycoon's new girlfriend brings forth vandalism by an invisible perpetrator. Meanwhile, Clark volunteers to work with Lana on a school blood drive after she and Whitney have a fight.

The Kents take in a mysterious youngster who can read minds, after he is accidentally struck by their pickup truck while fleeing from a murderous thief. Meanwhile, Lionel Luther offers Lex a job in Metropolis, but Lex is skeptical of his father's generosity.

Lionel Luthor announces plans to close the LutherCorp plant in Smallville, but Lex won't let his father shut it down without a fight. Meanwhile, Chloe tells Clark that she and her father may have to move back to Metropolis so her dad can find a new job; and Whitney surprises Lana by enlisting in the Marines.

Clark tells Pete about his extraterrestrial powers after Pete finds Clark's spaceship and insists on hiding it in a shed in his own yard, but the craft is soon stolen by a scientist. Meanwhile, Lionel Luthor claims he wants to spend more time with Lex; and Lana is suspicious of her aunt's new boyfriend.

A teen who is kept locked in the basement of his parents' house during the day sneaks out at night and leaves love letters for Lana at her parents' graves. Meanwhile, Lionel Luthor hires Clark's mother as his personal assistant.

A woman arrives in Smallville and tells Clark that she's his biological mother and informs Lex that Lionel is the father. Plus, she wants Clark to take a DNA test to confirm her story. Meanwhile, Lana decides to meet the man who could be her biological father.

One of Clark's former adversaries returns to Smallville and causes a rift between Lana and Clark. Elsewhere, Lex accuses a woman he's dating of spying on him for Lionel Luthor.

Lex hires goons to plant listening devices in his father's Metropolis office, but things go awry when the thugs decide to rob the tycoon's vault instead and end up taking two hostages: Lionel Luthor and Martha Kent. Meanwhile, Lana learns that her biological father's wife has agreed to meet with her, but the encounter proves to be a tense one.

Lionel Luthor is shot by an unknown assailant and Jonathan Kent is arrested for the crime after the police find him with a gun and a bottle of tequila. Meanwhile, Lex does some digging of his own and begins to suspect that someone else pulled the trigger, but his reluctance to share this information leads to a clash with Clark.

Clark witnesses a popular Smallville baseball player steal a shipment of refined kryptonite from a LuthorCorp truck to enhance his athletic abilities. Meanwhile, Lana's relationship with her father improves, while Clark's friendship with Chloe deteriorates.

In the conclusion, crime boss Morgan Edge tracks down Clark to get the package he took from LuthorCorp. Elsewhere, Lex confronts Helen about what really happened the night his plane crashed.

Clark tries to prove Lex's sanity and prevent Lionel from forcing electroshock therapy on his son. Also, Lana meets a mysterious guy in the hospital while recovering from her injuries; and Clark runs into former enemies who plan to steal his strength.

Clark loses his sight and gains superhuman hearing, which he can't control, when he attempts to stop a jewelry-store robbery involving a teen with a powerful scream. Also, Clark learns that Chloe did research on him for Lionel; Pete is kidnapped.

Lionel makes a deal with Dr. Virgil Swann, hoping to uncover the secrets behind the Indian cave drawings. Elsewhere, Jonathan continues to struggle with his own mortality; and Lex works as an informant for the FBI against his will.

A chemical accident at the LuthorCorp plant gives Chloe the ability to make people tell her the truth. When Lionel learns of Chloe's new power, he tries to exploit it by forcing her to uncover Clark's secrets.

Clark decides to reveal his secret to Lana, hoping his show of trust will persuade her not to leave Smallville, but before he can tell her, she is kidnapped by a childhood friend who has developed the ability to pass through objects. Meanwhile, Lionel learns that Lex is working with the FBI.

A mysterious stranger with powers similar to Clark's arrives at the Kent farm and tells the Teen of Steel that she's from Krypton and was sent to bring him home. Elsewhere, Lana says her goodbyes before her trip to Paris; and Lionel, who's locked in a prison cell, prepares for his day in court.

Clark switches bodies with Lionel after Clark interferes with the exchange of a Kryptonian stone that was meant for an unsuspecting Lex. Consequently, Clark takes Lionel's place in prison, while Lionel takes advantage of his newfound freedom---and superhuman abilities.

The town's residents are infected by a toxin that causes unconsciousness and horrific nightmares when the LuthorCorp plant loses control of the dangerous substance. Meanwhile, Lionel's conviction is overturned, but he feels he deserves to stay in prison.

A teen with teleportation abilities who was obsessed with Clark is released from the Belle Reve asylum and tracks him down. Though apparently reformed, she manipulates Clark's feelings for her using red kryptonite. Meanwhile, Lionel tries to convince Lex that he's a changed man; and Lana confronts Jason about the breakup.

Clark takes in a dog with superpowers after Lois accidentally hits the pooch with her car. While looking for its owner, he discovers the dog was part of a LuthorCorp experiment and was being used to commit crimes. Elsewhere, Genevieve is revealed to be the person who helped free Lionel from prison.

Lois's younger sister, Lucy, arrives in town, and Clark learns that she has a shady past when he catches her stealing money from the Talon's register. Also, the ancient stone is taken from Lana's apartment, and Jason suspects Lionel.

A kryptonite-based explosion at the Luthorcorp lab creates an evil clone of Lex, and the sinister twin tries to prevent the process from being reversed by taking drastic measures, which include imprisoning Lex in the basement of his own mansion.

Lana and Clark take care of a baby they find in a crater and are shocked when he ages seven years right in front of their eyes. They then turn to Lex for help, hoping LuthorCorp labs can find a way to curtail the child's growth. Elsewhere, Genevieve confronts Lionel about the missing sacred stone.

A teen who has the power to turn people into stone wants to stay in high school forever, so he keeps students captive in a fake school that's built to look like Smallville High. Elsewhere, Genevieve and Jason threaten to kill Lex if Lionel doesn't give up the sacred stone.

Clark is forced to steal a serum from a heavily guarded LuthorCorp research facility by three superhuman Belle Reve escapees who are holding Lana and his parents captive.

Arthur Curry, better known as Aquaman, arrives in town to destroy a new sonar weapon designed by LuthorCorp. Meanwhile, Clark meets Prof. Milton Fine, a.k.a. Brainiac.

Lana pledges a sorority, unaware that its members are vampires. Elsewhere, Chloe sets out to impress the Daily Planet's editor-in-chief; and Lex threatens to have Prof. Fine fired if he continues to research LuthorCorp.

One of the volunteers on Lex's campaign staff is far too devoted to the cause, and takes matters into her own hands, hatching a scheme that even shocks Lex. Meanwhile, Martha makes a deal with Lionel.

A mysterious female vigilante stalks the Suicide Slums, and her path crosses Clark's as they both seek the same criminal; meanwhile, LuthorCorp experiences a shakeup.

Clark befriends Victor, the unwilling victim of a cybernetics experiment at LuthorCorp, but Lex wants him back. Meanwhile, Martha may be the target of blackmail.

Lana gets hooked on a dangerous serum made of green kryptonite; Clark searches for Prof. Fine in Honduras, and discovers Lionel knows his secret.

Lionel Luthor finds himself the victim of a mysterious tormentor who uses a series of life-or-death riddles and puzzles that eventually pit Lionel against Martha Kent.

Suspicions about Lionel Luthor's intentions are raised when Clark and Martha receive ghostly visits from Jonathan, who tells them that Lionel must die. Meanwhile, Lex's trust in Milton Fine is taxed when Fine demands the vaccine.

Clark's Kryptonian origins sow seeds of sorrow and destruction on Earth as forces affecting Lex, Lionel, Lana and Clark are set in motion, culminating in the moment for which all his trials have prepared him.

Lex disappears in front of Lana's eyes but nobody, including Lionel and Lex's security team, seems to believe her; Clark finds another refugee from the Phantom Zone---and this one eats human bones.

The Green Arrow, Impulse, Aquaman and Cyborg try to destroy LuthorCorp's secret laboratory, but Impulse is captured and tortured by Lex, prompting the others to join forces as a team to rescue him.

Lana is shot after secretly meeting with Lionel at the Daily Planet. As Jimmy studies photos of the scene, he's knocked unconscious and dreams of a 1940s version of Smallville. Meanwhile, Clark discovers why Lana married Lex.

In the sixth-season finale, Clark learns how Lionel got Lana to marry his son; Lana tells Lex that it's over; Martian Manhunter helps Clark stop Lex from finding the last Phantom Zone wraith, hoping to keep him from building his army of super soldiers; and Lois gets into serious trouble when she tries to investigate the secret lab.

Clark saves the life of a starlet on a film shoot in Smallville when a stunt car's brakes fail, but what happened was no accident. Meanwhile, Lionel finds himself the victim of a surprising captor.

Lionel kidnaps Clark and holds him in a kryptonite-lined cell at a Luthorcorp facility; Chloe and Lana confront Lionel, who blames Lex, and they then take Kara to the Fortress and plead with Jor-El to restore her memory so she can save Clark.

Clark, through a series of messages sent by Kara from Krypton, discovers what Earth would be like had he never arrived: Jonathan is still alive; Lex is the president; the Luthors have raised Kara; Lana is happily married; and Chloe and Lois are ace reporters.