Season 3 Of Smallville

Lex managed to survive the crash and ended up on a deserted island. He met a man, Louis Leery Jr., who suggested that either Lionel or Helen set him up to die in the plane crash. Louis, however, revealed himself to be quite insane, forcing Lex to remain on the island with him and thwarting all his attempts to be rescued. Three months later, Lex found a skeleton that turned out to be the remains of Louis' father. Louis admitted to killing his father, but said the old man deserved it because he was always taunting him and chipping away at his sanity until he couldn't take it anymore. He then attacked Lex and chased him, but Lex turned the tables and hacked Louis to death with a machete. When he was rescued, Lex was shocked to learn that there hadn't been anyone else on the island. 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 and pulled a gun on his father, 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. Later, Lex was shocked when he learned that Helen had lied to everyone and told them that the plane had been caught in a storm, the pilot had disappeared, and there was only one parachute, which Lex heroically offered to her in order to save her at the expense of his own life. Lex confronted Helen, who tearfully told him that she had awoken on the plane to find the pilot gone and the plane about to crash, realized he had been drugged but was unable to wake him. Afraid for her life, Helen took the only parachute and left Lex to die. She offered to have the marriage annulled, but Lex told her he wanted a second chance with her. However, when they went on yet another plane ride, Lex confronted Helen again, armed this time with the truth. He'd done his research and discovered 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. Helen had the original pilot killed, snuck her own on board, drugged Lex, and was dropped off at a nearby island and later returned to Smallville. The pilot flew Lex hundreds of miles off course into a storm hoping he'd be killed, and then took the only parachute and jumped off the plane, only to find that Helen had rigged the parachute to fail so that he'd fall to his death. 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. Throughout the third season, Lex continued to want nothing more than to have a real family with his father, and later admitted to Chloe Sullivan that all he wanted was for his father to love him.

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. Seeing this as a way to get out from under his father's thumb once and for all, Lex went to the police, 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, and while still in Belle Reve, he had kept Clark's secret.

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 meteor rock. 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 previous.

Later, Lex was informed by Chloe of his grandparents' murder at the hands of his father and Morgan Edge, and got the information to the FBI. As the year ended, Lex's room about Clark was found out by Clark, and 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.