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- "It's my birthright! After all my sacrifices, after all the pain, I finally understand. I was being prepared for a much greater destiny. Everything led me to this moment." – Lex Luthor to Clark Kent, Arctic
As the dam was about to burst, Lex watched as the water washed the police car he was in. Fighting to stay alive, Lex saw an angelic girl in the river, and she later saved him by bringing him to shore. Lex managed to catch a glimpse of her before she flew off. Lex was found later and decided to turn himself in. Lex was approached by Bizarro in need of finding Clark and killing him. Lex confessed and was incarcerated. Lex willingly went to jail for Lana's murder for a short time, until someone else confessed.
Lex was released because Lionel paid a terminally-ill employee from LuthorCorp to confess to the crime. Lex believed Lana was not really dead and questioned Chloe, but she had nothing to say to him. Lex hired private investigators to use voice-recognition software on cellular phone lines and Lana was located in Shanghai, China. Lex subsequently tracked Lana down and confronted her and she revealed that she discovered his experimental clone he had produced and used it to frame him. She claimed she allowed herself to be found and tried to shoot him but was unable to pull the trigger. Lex was resigned and apologetic for victimizing her and informed her that she could come back to Smallville and divorce him with no resistance from him.
Lex began working with Dr. Curtis Knox on a way to cure metahumans. Lex started questioning Knox's experimentation of using their organs and discovered that he was killing his patients. Knox almost killed Lex but he was saved by Clark. Lex then helped Clark locate Knox's latest victim, Chloe, before Knox killed her.
When the movie version of "Warrior Angel" came to Smallville, Clark went to Lex for help when crazed fan Ben Meyers tried to kill the movie's leading lady. Lex used his extensive "Warrior Angel" comic collection and knowledge to help Clark figure out the fan's motives. Lex later confronted Ben and asked him what he knew about Clark's secret, but Ben would not tell him anything.
Lex was revealed to be responsible for making Grant Gabriel an editor at the Daily Planet. He told Grant to break off the relationship he had with Lois. Although Grant said that he was Julian Luthor, it was later revealed that he was actually a clone of Julian when Adrian Cross used Lois to expose Project Gemini. He also revealed that he had purchased the Daily Planet.
After it was revealed Lex cloned his deceased brother to have someone to love him and to be a companion, he had warned Gabriel to stay away from Lionel, under the guise that Lionel would reject and hate Gabriel. Instead, Gabriel, resentful of Lex's control of his life and how he was created confronted Lionel with what his son had done. Instead, to Gabriel's amazement, Lionel, while truly repulsed by what Lex did, nonetheless didn't hold it against Gabriel and actually accepted him as his son. After learning that Grant went to Lionel and that Lionel knew about him and to his hurt Lionel preferred "Julian" over Lex despite being repulsed at Lex for creating him. Later, Lex tried to force the two to stay away from each other by warning Gabriel to do so and firing him from the editor position at the Daily Planet. However, when neither obeyed, Lex felt that he was forced to have Grant assassinated, not being able to stand that Lionel loved him more than him. He had an assassin pose as a mugger to rob them. The assassin shot Gabriel in front of Lionel, and he died in Lionel's arms. The assassin text messaged Lex that the job was done. Lex, in numb shock, walked to his patio in the rain and screamed skyward in grief and loneliness over what he had done.
Lex received the DVD that had incriminating information on it from Black Canary. He payed her and offered more for her if she brought in Green Arrow. Once Black Canary appeared, knowing he tricked her, Lex shot her and forced her to tell him about the Green Arrow, only to start an intense fight with the heroic, green archer. He later got stabbed by a dagger from the Black Canary, as he watched both of them leave.
Lex and Lois had managed to track Kara Kent down into Detroit, Michigan. To save both Lois and Kara, he shot Finley; unfortunately, Lex ended up with a bullet in the head. However, he was healed and saved by Chloe. Lex managed to bring Kara back to Smallville to try to regain her memory and discover the Kent family secret.
Lex had the computers in the Daily Planet, especially Chloe's, connected to his so he could see what they were doing. Lex used blackmail to get Pete to steal Kara's Kryptonian bracelet from Lionel's vault in return for protecting Chloe's secret as a metahuman. When Pete returned, Lex started torturing Pete about the bracelet. After getting knocked out by Clark, he was talking to his assistant about the first meteor shower when Kara came into the room to ask if she could stay with him since she couldn't trust Clark and Lana anymore.
Lex planned to get Kara's memory returned so he could have answers to the questions that plagued him. He later met his childhood friend Patricia Swann, who informed him about Veritas. Lex later demanded to be told about Veritas, but Lionel did not give in. Lex had a hand in the assassination of Patricia as he had her necklace. He later remembered a memory in which his father is meeting with the secret Veritas society.
After Lionel returned to his office, Lex questioned his father about Veritas and the reason they were in Smallville on the day of the meteor shower. He then stole his Veritas key and later pushed his father out of his office window. When the authorities came, Lex made up a story about hearing him fall to his death outside of his office. Somewhat overwrought with guilt, Lex saw his childhood personality Alexander questioning him about what he had done. He then later returned to the mansion, and remembering every trip he went on with his father, as he told a story to his assistant. Lex found a Veritas key in Chloe's desk at the Daily Planet, and had her fired. As he found Clark in the mansion, the two had a heated discussion and argument about their friendship and their own fathers. While he was being tortured with guilt by his childhood personality, Lex did away with it, for he claimed it made him weak. Lex made Lionel's funeral cut down to only one participant, him but Clark payed his respects anyway.
As he was ready to fly over to Zurich, Lex was halted by one of his security men who told him that there was a problem between him and the government, but Lex managed to make it to Zurich where he opened the Veritas safety deposit box and found a strange cryptograph. When Chloe was in danger by the government, Lex came to the rescue and ended the investigation for Jimmy. Lex reminded Jimmy that because he thought of Jimmy and the Daily Planet employees were like family to him, family should help each other out when needed.
Lex offered Clark his help with saving Lana, but neither one could do anything.
As Lex had one of North America’s greatest cryptographers examining the Veritas map, he felt impatient with him and was forced to have the man examine it in his laboratory. After he left, Lex was attacked and had Kryptonian symbols carved into his chest. Lex later awakened to find himself in the hospital with the symbol on his chest. He then went to the cryptographer and killed his attacker. Lex learned from the cryptographer about the maker of the map and its possible location in Montreal. Lex had found the clock, placed the map inside it as it played a familiar melody to Lex, and released a black Kryptonian pentagon piece. He was then confronted by Edward Teague and the two fought over the secret of the Traveler and the Destroyer. After returning home, Lex put the clues together he had gathered about Veritas and discovered a device placed in the chimney of the Luthor Mansion. Bringing the pentagon piece and device together, showed an image of the Earth and exact coordinates to a certain point placed deep into the Arctic Circle.
As he was searching for a specific location in the Arctic, Lex had Jimmy keep Lois occupied with a fake story as he threatened to put Chloe in jail. Brainiac (posing as Kara) told Lex that he was meant to destroy the Traveler (Clark) to protect the Earth. Lex then left for the Arctic and had the Department of Domestic Security go after Chloe when Jimmy failed to do his bidding. Lex then arrived in the Fortress of Solitude, with Clark arriving shortly after. The two had a brief confrontation, then Lex placed the Control Device in the console of the Fortress, and the Fortress started crumbling down on them with him and Clark inside.