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- "You haven't changed, Rachel. You're still irrational." - Lionel Luthor, Lineage
Lionel was rescued by Lex and taken to the Smallville Medical Center, where he underwent surgery that saved his life, but left him blind. Lionel then went into therapy, and moved into the Luthor Mansion with Lex as he refused to be gawked at by others.
Sometime later, he redecorated the mansion and conducted business there, much to Lex's annoyance. Lionel also met Clark Kent who, under the influence of red kryptonite, proceeded to mock Lionel. Later on, Lex had everything put back the way it was before Lionel moved in and laid down the law with his father, causing Lionel to wonder aloud if Lex discovered the value of directness from his friend Clark as he fingered flattened bullets that were blocked by Clark earlier.
Lionel hired Martha Kent to be his assistant. However, he found himself attracted to Martha. Also, his sight had returned and tried to fake being blind for a couple of weeks until Lucas Luthor exposed the truth.
When Lionel's ex-lover Rachel Dunleavy came back into his life, she kidnapped Lex to force Lionel to acknowledge Clark as their illegitimate son. Rachel angrily stormed in on Lionel, accusing him of switching the DNA samples and forcing her to give up her child. Unbeknownst to Rachel and Lionel, Clark and Pete broke into the lab and switched the DNA samples. She threatened to expose him; Lionel flirted with her and offered to get her psychiatric help.
When Lionel learned that Clark had a mysterious connection to the Kawatche Caves, he did all he could to figure out who Clark really was and, more importantly, where he came from.
Later on, while in Metropolis, Lionel gave Martha a beautiful watch and told her that she had been promoted and had her own office there in Metropolis. Martha turned the promotion down, but they were held hostage before she could leave. Shortly after Martha quit her job, Lionel was shot by Sheriff Ethan Miller, but recovered and returned to Metropolis.
Lex located Rachel's missing child, Lucas, and introduced him to Lionel. Lionel revealed that he knew all along where Lucas was. It´s revealed that Lionel was not blind anymore and was confronted by Lex.
A few months later, Lionel offered Chloe Sullivan a column at the Daily Planet in exchange for her helping him get information on Clark. At first, Chloe turned him down, but then she reconsidered his offer.
At an attempt at peace with Lex, Lionel offered him a honeymoon trip, but got control of the Kawatche Caves. At the same time, Lionel made a duplicate of Clark's spaceship key manufactured from the pattern on Dr. Frederick Walden's palm and refined kryptonite, and planned to insert it into the hole in the cave. Unfortunately, the kryptonite key was stolen by Clark with assistance from Pete Ross.