After killing Lionel, Lex found the locket to be empty, as Lionel had left Chloe the Veritas key earlier that day. Lionel also left a Kryptonian message for Clark, who realized that Lionel, like Jor-El and Jonathan Kent, had played an important role in making him the man that he is. Lionel had indeed changed for the better.
Lionel's final message to Clark
Following Lionel's death, Clark angrily confronted Lex about Lionel, and the two had an intense argument. Clark accused Lex of murdering Lionel, while Lex made it a point to repeatedly mention how much Lionel preferred Clark over himself and stated that both Lionel and Jonathan felt that Clark was "the kind of son a father could be proud of." Clark then pointed out that both Jonathan and Lionel would have given the same affection to Lex if he had tried to be a good son. When Lex suggested that Clark was responsible for Jonathan's death, Clark said he had proof that Lex killed Lionel, which visibly shook Lex.
Lex and Clark at Lionel's funeral
Later, when Lex decreed that everyone but him was banned from Lionel's funeral, Clark, in a lone act of defiance, attended Lionel's funeral. Clark finally cemented the father/son bond he had with Lionel when he sprinkled dirt over Lionel's grave, the same thing he did at Jonathan's funeral.