- "In my lifetime, I have known many famous and powerful men: presidents, sultans, kings, and I believed that I was superior to them all. But I've come to know the truth, Kal-El. My greatest accomplishment is that I have dedicated myself to protecting your life and serving you. For that I am grateful." - Lionel Luthor, to Clark, Descent
Lionel washed ashore after the dam broke, and was then dragged away by a mysterious figure. No one knew of this, so he was presumed dead by Lex and the media.
Sometime later, Lionel finally awoke to find himself chained to a bed by a woman named Marilyn. He managed to get loose, but was knocked out by Lana. After Lex tried to free Lionel, Marilyn had a gun pointed at his son, and Lionel snuck up behind her and beat her to death. Lionel went to see Lana at the Kent Farm, and knew she was behind his disappearance. He warned her not to continue with her sense of retribution or something bad would happen.
Lionel was later attacked by Zor-El, who threatened to kill him if he didn't tell Clark to trust him. Lionel refused, claiming that Clark was following his own destiny. Clark showed up and saved Lionel, who was later hospitalized with minor injuries.
Grant Gabriel went to Lionel, and told him he was the clone of his deceased son Julian Luthor. Lionel was proud and happy to see the man his "son" had come to be; unfortunately, he was disgusted that Lex had done this. When Lionel took Grant to a steak restaurant in Metropolis, Lex had an assassin find Grant and kill him in front of Lionel.
Still angry and mourning over Grant's death, Lionel asked for Lana's help in bringing down Lex for what he had done, threatening to tell Clark about her role in the death of Casey Brock if she didn't help him. Lana told Clark the news himself, and later came to Lionel's office and told him she had no information. She also said she was not going to spy for him any longer.
Lionel let Clark and Chloe know what happened to Lex, and watched over Lex and Clark as Project Intercept allowed Clark to go inside Lex's mind. After Lex died, Chloe healed him, and Clark awoke to find Chloe dead in Lionel's arms. Lionel was confused when Clark told him to bring Chloe to her apartment without taking her to a doctor. Later, he told Lex that he loved him.
While in his office, Lionel received a letter from Veritas and started fearing the worst. He went to meet Patricia Swann, the daughter of Virgil Swann, and was suspected of murdering Oliver Queen's parents as well as Dr. Swann. As it turned out, it was Lionel who staged Clark's capture by Pierce. Lionel threw the suspicion off of himself to Lex when Lana and Chloe came to him for answers. Wanting the evidence to link him to the murders of the Veritas members, Lionel agreed to set Clark free, but Pierce betrayed him and intended to kill Clark. After Kara saved Clark, Pierce prepared to shoot them with kryptonite tasers but Lionel hit him with a pipe, killing him. As Lionel attempted to explain to Clark about Veritas and keeping him in a kryptonite cage, he realized that his friendship with Clark had been greatly damaged.
Lionel was later ambushed by Lois and Jimmy Olsen as they questioned him about the murder of Patricia Swann; he admitted nothing. He had left evidence to Lana proving that it was Lex who was responsible for Patricia's murder. While it was probably Lionel who arranged for the Queens to be killed, all evidence pointed to Lex as the murderer of Patricia Swann. Lionel claimed to be a changed man after he was chosen to be Jor-El's vessel, hoping that by protecting Clark now, he might atone for some of his past sins.
Lex eventually came to believe that the LuthorCorp plant in Smallville was only a cover-up to see "The Traveler," and confronted his father about this in his office. Lionel tried to warn Lex not to press him about Veritas, telling his son that Lex was actually the Traveler. Unfortunately, Lex did not believe any of this, and shattered the office window by shooting it. Lex tore the locket off of his father's neck and pushed him out the open window, letting him to fall to his death.