- "Lana, with the life I've led, I go to bed praying every night that I don't get what I deserve." – Lex Luthor, Hydro
Lex managed to get free from Zod when Clark returned from the Phantom Zone and used the Crystal of El to separate Zod's spirit from Lex's body, restoring Lex back to normal with no recollection of the destruction he caused while possessed by Zod, other than what Lana told him.
Lex had Lana move into the Luthor Mansion due to Metropolis University's dorms being closed. Shortly after, he was kidnapped by Orlando Block. Block threatened Lex until he told him about a serum that would supposedly endow a person with superhuman strength, and brought in Lana to be the test subject. Luckily, Lex got loose and killed Block. However, the laboratory caught fire, but Clark secretly put it out and Lex and Lana were saved.
Lex hosted a charity costume ball to raise money for the families and victims of Dark Thursday, and consummated his relationship with Lana. Later, he enlisted Lionel's help in testing Lana's loyalty about their decision with the Kryptonian black box. Lex later encountered his old classmate Oliver Queen at their Excelsior Academy class reunion, and he had to come to terms with the events that happened years ago. Shortly after, Oliver's old friends were killed in violent and mysterious accidents that pointed to Duncan Allenmeyer.
Lex was confronted by Jimmy Olsen with evidence of his meeting with Dr. Groll to discuss the Kryptonian black box and had Jimmy fired from the Daily Planet. Lana grew tired of Lex's obsession with the box and gave Lex an ultimatum: the box or her. When the box was destroyed by the Zoner Baern, Lex chose Lana, but she suspected that he only chose her by default.
Lex was shot with an arrow by the Green Arrow. As Lex lay dying, Clark gave him a healing drug to save his life. In one of his lowest moves, Lex seemingly had the maker of the drug murdered and had a teenager from the Halfway House blamed for it. As all of this was going on, Lana learned that she was pregnant. Feeling that her relationship with Lex had begun to go downhill because of Lex's dishonesty and mistrust, Lana seemed devastated by the pregnancy.
Lex got stuck in a different "frequency" of reality by Bronson, a patient from Level 33.1. He was unable to be seen or heard by anyone, unless by radio. While Lex was in a different frequency, Lana told him she was pregnant, and after he stopped Bronson, Lex asked her to marry him. However, he didn't want to pressure Lana into an answer and waited several weeks for her to respond. Lana confessed to Chloe that something about Lex made her hesitate, and she still had feelings for Clark. When Lana's comments were published in the gossip column of the Daily Planet by Linda Lake, Lex had to face the reason for Lana's hesitation. However, Lana chose to resolve her feelings for Clark and accept Lex's proposal.
Clark and Lois, both infected with an aphrodisiac made with red kryptonite, burst in and disrupted Lex and Lana's engagement party. When Clark grabbed Lana and took her to the Kent Farm, Lex came after him with a gun. Clark knocked the gun out of his hand and tried to strangle Lex, until Lex grabbed a chisel and tried to stab him at the same time Martha disabled Clark with a meteor rock. When Lana feared she was being stalked, Lex did all he could to ensure her safety, but was angered by Lana's decision to hide out at the Kent Farm. He hand-delivered Clark a wedding invitation so that Clark could see what he lost. Lex worked with Dr. Robert Bethany to manipulate Tobias Rice into identifying meteor-infected people. He supervised the kidnapping and experimentation of Chloe.
On his wedding day, Lex confessed to Lionel that he was afraid Lana would not show up. That same day, Dr. Langston (Lana's obstetrician) attempted to blackmail Lex and threatened to tell Lana every detail of her pregnancy. In a fit of rage, Lex accidentally murdered Langston, but Lionel found out and berated him for doing such a sloppy job of cleaning up his messes. Due to Lionel's coercion, Lana did indeed show up and she and Lex were married on February 24, 2007.
A week after the wedding, Lana miscarried and fell into a deep depression. Lex seemed concerned for Lana's health and state of mind, but he was seen burning her medical files. Lana continued to pull away and when she was hospitalized again, she learned that her pregnancy was faked due to synthetic hormone injections. She believed Lex to be responsible, but did not confront him and continued to pretend to be his devoted wife. Lex became increasingly preoccupied with his Level 33.1 project.
He obtained the extraterrestrial body of the fighter Titan and had Moira Sullivan transferred, he administered a drug that brought her out of her catatonic state. She was able to control her daughter Chloe to steal a flash drive from Lex, so Lex manipulated Moira by kidnapping Chloe too. Under her mother's mind control, Chloe shot Lex in the face, but Clark arrived in time to save Lex and rescue Chloe and her mother. Chloe attempted to write an article exposing Lex's project, but he calmly threatened to have her thrown in jail or killed, also possibly hinting to keep her in 33.1.
Lex was trapped in an underground tunnel by Jodi Keenan. At Lionel's request, Clark attempted to save him but was also trapped by the green meteor rock lining the tunnels' walls. While attempting to escape, Lex and Clark analyzed the breakdown of their friendship and Clark revealed that Lana was going to leave him. However, they realized that they would only be safe if they helped each other. When Clark was trapped under rubble, Lex freed him. They managed to escape through a ladder leading up to the surface. The purpose of the tunnels was revealed to be an underground laboratory leading to Reeves Dam for Project Ares which had just completed its first prototype: Wes Keenan.
Using Titan's alien DNA of, Lex turned Keenan into a super soldier with many different meteor powers and tested him in the tunnels. Lex met with Senator Ed Burke to inform him the progress of Project Ares, but Burke wanted it canceled, threatening to release incriminating evidence about LuthorCorp. Lex used Wes to kill the senator, but Wes unexpectedly ran into Lois and was able to circumvent his programming. Lex was unable to regain control of Wes before he battled Clark. Wes was badly damaged and chose to die rather than be under Lex's control. Lex studied Wes' body but was unsatisfied with his results.
Lex decided that Project Ares would only be successful with a living DNA donor and began to track the last loose Phantom Zone wraith Bizarro. When Lana decided to leave Lex, he assumed that Clark had finally come between them. Lana maintained that his betrayal over the fake pregnancy was the real reason and declared that he would have to kill her to keep her. Lex claimed to not know anything about the scam and slapped Lana across the face, thus putting an end to their short and turbulent marriage. Bizarro was apprehended in the body of a young boy but Lex and his team lost control. Lex narrowly escaped death but while fleeing Reeves Dam, he was arrested for Lana's murder.