- "I know, I know. The methods I have to use seem cruel, heartless but the truth is I am using them to protect you." - Lionel Luthor, to Clark Kent, Phantom
Lionel managed to save Chloe and witnessed General Zod, now inhabiting Lex's body, take flight with Lana in tow. He told Chloe that his connection with Jor-El was gone, and that he was no longer influenced by him. When Chloe opted to go back to the Daily Planet, Lionel gave her his gun to use in case of danger, and went to Martha to help and find the Kryptonian dagger, which Lana took to use on Zod.
Even though his connection with Jor-El was gone, Lionel still remembered a few Kryptonian symbols. He kept his information about the Kryptonian symbols to himself, and informed Clark and Martha about everything happening with Lex. Lionel met Oliver Queen, and welcomed him to Metropolis. Later, Lionel's help was enlisted by Lex to test Lana's loyalty. Lionel accidentally admitted his feelings for Martha, and he attended Thanksgiving dinner at the Kents.
Over the course of the season, Lionel became more and more of a father figure to Clark than even his own son Lex; he often found himself being more encouraging and supportive of Clark than he ever was to Lex. This was not lost on Lex, who questioned Lionel on it; Lionel replied that Clark was "the kind of son a father can be proud of," furthering his preference of Clark over Lex. He even went as far as to call Clark "son," a name he formerly used only with Lex. For his part, Clark, somewhat begrudgingly, came to reciprocate the father/son bond Lionel had for him. He often came to Lionel when he needed advice, and found that only Lionel could point him in the right direction.
Later, Lex spoke to Lionel about Level 33.1. Lionel was concerned that the press would find out that Lex was experimenting on metahumans and managed to discover there was a person with superhuman speed. He was confronted by Lex and thought that Clark was in Mexico, but it turned out to be Bart Allen, who was the superhuman speedster. Lionel later covered for Clark when he was suspected in being in the Project 33.1 facility blown up by the "Justice League."
When Clark was attacked in his barn by an Zoner and put in an illusion world, he found that his adoptive mother was married to Lionel, and Lionel was the one who wanted to help Clark with his mental state and put Clark in the mental hospital.
On the day of Lex and Lana's wedding, Lionel found Lex at LuthorCorp alone, and asked him what he'd be willing to do to make sure the wedding happened; Lex answered that he'd do anything. Lionel then left as Lex received a phone call; he listened at the door when Lex told the caller that he would meet him later. When Lionel went to see Lana, he read her letter and realized that she didn't intend to marry Lex, correctly guessing that she knew Clark's secret. Lionel revealed to Lana that he knew Clark's secret too, but that he also knew Clark's weakness; he then told her that if she didn't marry Lex, he would kill Clark. Lionel met Lex after the ceremony because he knew that Lex killed Dr. Langston. Lex offered him control of LuthorCorp or even Level 33.1, but Lionel just said Lex would know when it was time for him to collect.
When Lionel was severely injured in an explosion caused by Jodi Keenan, Lana forced him to tell her the reason he forced her to marry Lex; he told her that it was to protect Clark. Lana later forced Lionel to tell her how he was protecting Clark; it was not yet been revealed if he told her the truth or not.
Lionel had learned that Lois Lane had stolen a cigarette carrier from the crime scene where had Lana been shot, and crept into her apartment to retrieve it. When she came in, Lionel took it and saw that there was a flash drive inside it; he used it to see that Lex was working with Senator Ed Burke on Project Ares.
Lionel was watching a video about a phantom attacking a reporter in Patagonia, and translated more Kryptonian symbols into the word "mirror." Clark then came in and accused Lionel of having Lana marry Lex.
Lex demanded that Lionel get out of his life, but Lionel did not oblige. Later, Lionel was confronted by Clark, who had discovered the truth about Lex and Lana's wedding; Clark was about to kill him until Martian Manhunter stopped him, telling him that Lionel was an emissary of Jor-El. He then explained the reason why he had Lana marry Lex: so Lana could get close to Lex to get information from him.
Lionel went to talk to Lana before she left Smallville and saw her getting in the car; it exploded with her in it. Later on, he told Clark about what happened, and begged him not to do what he would later regret, but Clark was too grief-stricken to listen. Lionel went to Reeves Dam to stop Clark from hurting Lex, taking a piece of kryptonite with him, but ended up using the kryptonite against Bizarro; this only made the phantom stronger. Bizarro then threw Lionel against the dam wall; Lionel was left unconscious as the dam cracked and began flooding.