- "There's so much of my own life I can't explain. I've survived countless brushes with death, and it all started with this car crash. If I'm guilty of anything, it's that I've inherited my father's eccentric curiosity for the unexplained." – Lex Luthor, Covenant
Lex managed to survive the crash and ended up on a deserted island where he spent over three months. In the island, Lex met Louis Leery Jr., an insane individual that thwarted all his attempts to be rescued. When the man attacked Lex and chased him, Lex hacked Louis to death with a machete minutes earlier of being rescued. Lex was shocked to learn that there hadn't been anyone else on the island and that he had a breakdown while on the island and imagined the whole incident; it was all a manifestation of Lex's own hatred of his father and his struggle with his humanity.
When he returned to Metropolis, Lex confronted Lionel at LuthorCorp accusing him of setting him up to die. Lionel told Lex that it was Helen who had tried to murder him, but Lex refused to believe him. After learned that Helen had lied to everyone about the circumstances of the crash, Lex planned his revenge. When they went on yet another plane ride to try to rekindle their marriage, Lex confronted Helen, revealing that she had been working for his father to spy on him after all, but that she'd decided to kill him instead, against Lionel's wishes. After Lex finished telling Helen what he knew, she pulled a gun on him. Lex fought with Helen over the gun and in the struggle the gun went off and the pilot was killed. Lex fought to get control of the plane, and while he did so, Helen escaped via parachute and was never seen again. Lex decided to try and get along better with his father and accept his destiny as a Luthor. He told his father, "If I were anyone else's son, I would have died on that island. If I keep my pride in check, I know there's a lot more I could learn from you.". He and his father agreed to run LuthorCorp together and work on their relationship.
Lex continued to want nothing more than to have a real family with his father, and later admitted to Chloe that all he wanted was for his father to love him. To ensure that Lex was psychologically fit to remain employed, Lionel requested that Lex submits to five therapy sessions, to which Lex eventually agreed to. Lex has his five sessions with Claire Foster. Due to his refusal to go into personal traumas, she suggested that Lex continue with more sessions. He refused to continue his therapy until he lost his temper and threatened Perry White.
During the course of the battle of wills between Lex and Lionel, Chloe uncovered evidence that Lionel had murdered his parents for the insurance money needed to start LuthorCorp. During his current therapy session, Lex described his time on the island and his encounter with Louis. His hesitation to bring up Louis stemmed from being afraid to confront his own darkness. Without Lex's knowledge, Claire called Lionel to mention that the childhood incident wasn't so isolated.
In an effort to get out from under his father's thumb once and for all, Lex went to the police with the information found by Chloe, but Lionel had learned of Lex's plan and had him drugged to make people believe that Lex was insane. Morgan Edge was in on Lionel's plan. While under the effects of the drugs, Lex witnessed Clark's abilities. Lex found himself in Belle Reve, where he was counseled with the other patients and given his daily medication. He insisted that the only reason he was there was due to Lionel trying to silence him.
After criticism from the other patients, Lex then went along with everybody in claiming that he was insane. During his time, he reflected on his discovery of Clark's abilities. He envisioned Clark freeing him and going with him to take revenge on Lionel. After a while he realized that all he wanted was to exploit Clark, and then vowed to become a more trustworthy friend.
When Clark came to visit, Lex assured him that he kept the secret to himself. He requested for Clark to break him out, only to make a failed escape attempt. To prevent Lex from telling anyone else about his past or trying to stop him, Lionel requested that Lex be given electroshock therapy, which completely erased the seven weeks of his life. Later, Lex went to Dr. Lawrence Garner, seeking his help in regaining his memories. He underwent an experiment process which involved being lowered into a tank of liquefied kryptonite. Although he didn't regain memory of the past seven weeks of his life, Lex did regain his true memories of his younger brother's death at the hands of his mother years previously.
Later, Lex was informed by Chloe of his grandparents' murder at the hands of his father and Edge, and got the information to the FBI. As the year ended, Lex's room about Clark was found out by Clark. Clark, angered and hurt over the fact that Lex had been investigating him all of his life, ended their friendship. Though he was arrested by the FBI, Lionel proved to be especially brutal and tried to poison Lex in retaliation.