- "I wanted to see you, Lex, to say goodbye face to face. I have done many things in my life that I've come to regret. But there is one thing I'll never forgive myself. I never... said 'I love you.'" - Lionel Luthor, Transference
Lionel got a hold of the Crystal of Water, which he planned to use to switch bodies with Lex, but the attempt failed when Clark interfered, resulting in Lionel switching bodies with Clark instead. While Lionel used his newfound powers to attempt to regain his lost fortune and alienate Clark's friends, Clark arranged to have it all switched back to normal.
Lionel discovered that he was cured from his liver cancer and told Clark about the energy coursing through him that healed his liver. Ever since he returned to his body, with no memory of being in Clark's body and his liver completely healed, Lionel dedicated himself to helping others, to make up for his past deeds. But, he didn't intend to leave prison, for that was his punishment and he accepted it.
When Lex was framed for killing a woman after a one-night stand, Lionel helped Clark search for the proof needed to help Lex, meanwhile falsely implying that Lex had a perverse fetish. Lionel was released from prison and his conviction overturned thanks to his mysterious benefactor, who happened to be Genevieve Teague.
Lionel came to visit Lex and told him he wanted to reconcile, as well as make the world a better place for everyone. Lex didn't listen to Lionel, but decided to let his father use the guest house at the mansion. Lionel later told Lana Lang about how Margaret Isobel Thoreaux was using her to get the Stones of Power, and gave Lana a map of China, saying Jason Teague was there with Lex attempting to find the Crystal of Air. He also let her and Clark use the LuthorCorp plane to get to China.
Lionel's completely peaceful nature was shattered when he faced Alexander, Lex's evil counterpart. After that encounter, Lionel revealed his deceitful nature once again, blackmailing Lex into giving him the Crystal of Air (which Lana had) or else he would reveal Lana's killing of Genevieve Teague.
While Lex later tried to bargain with his father over the stones, the Crystal of Water that was in Lionel's pocket gave off a massive force of energy, putting Lionel in a coma. Lionel was placed in an upstairs bedroom. Before departing, Lex told Lionel that he was now the son Lionel raised him to be.