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The relationship between Jonathan Kent and Lionel Luthor has been predominantly hostile, which was not helped by Martha Kent's growing relationship with Lionel. Although she always remained faithful to Jonathan, there was always something between Martha and Lionel, which developed further after Jonathan's death.
After the 1989 meteor shower, Martha and Jonathan found Clark Kent along with his spaceship and deduced that he was an alien. Having wanted a child for so long but being unable to conceive, they decided to keep him. As they drove home they came across Lionel Luthor, who was distressed by the fact that his son, Lex Luthor, had lost all his hair in the blast from a meteor. This is where Lionel and Martha first met, as they offered to give him a ride to Smallville Medical Center.
Lionel was keen to show his gratitude and offered help whenever they should need it. They required help sooner than he expected, as the Kents needed to forge adoption papers for Clark. Lionel asked no questions but in return expected them to help him get a foothold in the community by convincing Pete Ross' family to sell their land to him. Subsequently, the relationship between the Luthors and the Kents was strained. This all was established in the season 2 episode, Lineage.
In Jitters, Lex introduces his father to Jonathan Kent, to which he turns and shakes his hand, saying, "It's been a long time." It is made clear that they know each other from sometime prior to the start of the show. The Kents' son is trapped inside a LuthorCorp facility and they want Lionel's help. Lionel insists he'll just let SWAT do its job. Martha pleaded with Lionel to get on the phone, outraged that he didn't seem to want to do anything and everything he could for all the children trapped inside. Lionel says he doesn't negotiate with terrorists. Martha says if Lionel won't talk to him, Jonathan will. Jonathan seems very willing, but Lex reminds them that it has to be Lionel speaking with Earl, because Earl (the hostage-taker) blames Lionel for his condition. Martha and Jonathan watch as Lionel makes a phone call to him.
Lex decides to go in once there is a gas leak and potential bomb. Martha, Jonathan, and Lionel all watch him proceed in.
Everyone is released, at one point, but Lex stays back on a suicide mission, sacrificing himself for everyone, so Clark stays back too to save him. Lionel is well aware his son (Lex) will be sealed inside with the gas leak, but he gives the approval to trap him in.
When Martha finds out Clark is there too, she pleads to Lionel that he open the doors in desperation for her son's life but Lionel explained that they were safety locked and couldn't be opened until the gas levels have gone done. Martha was shocked that Lionel wasn't prepared to help, especially as his son was in there too.
Then, Clark does something to make the gas levels begin to drop. Lionel, Martha, and Jonathan are all there to hear the shocking news.
Despite Martha's distrust of Lionel and Jonathan's open hostility towards him, Lionel was able to recognize that they were good people. When Martha came to collect money for the delivery of organic produce, she interrupted Lionel's tantrum about inappropriate personal assistants. She then commented on a news story about a business from the paper, which made Lionel realize that she had a good sense of the business world and offered her a job as his personal assistant at LuthorCorp.
Although she wanted to consult with Jonathan first, she was keen to take the job. Jonathan was not happy about this and, on her first day, the dangers of her involvement with Lionel became apparent when Byron Moore wanted revenge on Lionel for giving him meteor powers. Byron attacked the helicopter that Martha and Lionel were in and was only prevented from hurting them by Clark. Martha encouraged Lionel to take responsibility for what had happened to Byron and organised the paperwork for Lionel to commit funds to researching a cure. Martha seemed satisfied that Lionel was trying to become a better man with her help, although Jonathan remained sceptical.
As Martha continued to work for Lionel, they worked very closely together. Lionel trusted her implicitly and her working relationship with him began to influence her morals when she took Lionel's side over the dispute with the Kawatche Caves Lionel found her forthright and straightforwardness refreshing, as he reminded him of his dead wife. However, Martha eventually realized that she was not prepared to sacrifice her morals for Lionel and her job. When Lionel complained to Martha about Clark's protests at the construction site she decided to risk her job and took Clark's side. Lionel clearly found Martha too valuable an asset and did not sack her, despite her actions, indicating his growing feelings for her.
Lionel offered Martha an expensive watch as a present for her hard work. She felt uncomfortable taking it, clearly concerned that Lionel was starting to have feelings for her. Jonathan also became frustrated by the amount of time Martha and Lionel were spending together. She admitted to Jonathan that she enjoyed working for Lionel, but she was only interested in a professional relationship. Nevertheless, she sacrificed a romantic picnic with Jonathan for work, much to his disappointment. This led to Martha and Lionel being held hostage by burglars with Jonathan waiting nervously outside.
While trapped in LuthorCorp Plaza, Lionel and Martha confided in each other about their relationships with Lex and Jonathan respectively. This indicated the level of trust that they had established. This trust was broken shortly after when the burglars broke into Lionel's vault to reveal a huge collection of kryptonite bars and the key. Martha was appalled and, after they were rescued, wrote her resignation. However, Jonathan convinced her not to quit but to continue to work for Lionel in order to collect intelligence of his further projects that could pose a threat to Clark. Nevertheless, their relationship was destroyed when Jonathan became a suspect in the attempted murder of Lionel Luthor and Martha lost her job.
Jonathan had discovered the watch that Lionel had given Martha, which led to a heated debate. Jonathan was clearly jealous of Lionel's growing relationship to Martha and remained resentful of Lionel for forcing Jonathan into giving him a foothold on the community. Jonathan maintained that Smallville would be better off without Lionel. This argument had given Jonathan a motive for Lionel's attack. Ultimately, Jonathan was proved innocent, although the Kent's relationship with Lionel remained damaged for some time.
Martha and Jonathan had little contact with Lionel for a long time, as Clark discovered more of Lionel's criminal activities including wiping Lex's memories and having his parents murdered. Jonathan and Martha also became concerned when Lionel came closer to discovering Clark's secret by trying to get hold of his blood sample. This led to another confrontation between Jonathan and Lionel in the caves. They fought over the key and, despite Jonathan's warnings, Lionel continued to investigate the caves.
Lionel later discovered the starblade in the caves. When Lionel and Lex touched the Kawatche knife at the same time and it disappeared, just as the mythology said it would when it was touched by Sageeth, Clark was confused as to which one was his ultimate enemy. Despite the break down in their relationship and being aware of Lionel's criminal activities, Martha was more inclined to believe that Lex was Sageeth rather than Lionel, indicating that she still had a little faith in him.
Lionel was sent to prison for his past crimes and had no contact with the Kents until he was able to switch bodies with Clark and escape from prison. He then assumed Clark's life and, when he saw Martha, he immediately asked for a hug from his "mom", indicating that he still carried a torch for her, despite the amount of time they had not seen each other. Martha recognized that Clark was acting strangely but hugged him, which aroused Lionel and activated his heat vision. Confused and annoyed, Martha left.
Although she had been avoiding Lionel for a long time, she agreed to visit the prison when Clark-as-Lionel contacted her. Wary at first, Martha eventually was convinced that Clark was in Lionel's body and tried to organize a way to transfer them back. She tried to warn Jonathan, but Lionel attacked him before she was able to contact him. Nevertheless, Lionel and Clark were eventually switched back and Lionel claimed that this experience changed him. While Jonathan remained sceptical, when Lionel met Martha again, she was more trusting of him.
Lionel tried to offer Jonathan money to help Jonathan run for State Senator. However, due to Jonathan's previous turbulent relationship with Lionel, he did not trust him and declined the offer. Lionel persisted and offered the money to Martha, seeing as they had a better relationship. Although she remained friendly, Martha rejected the money out of respect of Jonathan's wishes. Nevertheless, after Lois admitted that without more money the campaign could not continue, Martha resorted to asking Lionel to fund the rest of the campaign. Lionel was pleased with Martha's decision.
After this, Lionel did everything he could to help Jonathan win, including buying information from Lex's associate who had been investigating the Kents. Lionel showed Jonathan this information after he won the election. Assuming that Lionel was trying to blackmail him again, Jonathan attacked him, which resulted in him having a fatal heart attack.
After Jonathan Kent's death, Martha was devastated. Lex discovered that Lionel had met with Jonathan shortly before he died. Aware of his father's feelings for Martha, he threatened to reveal the truth unless he was able to reclaim his share of LuthorCorp. In order to remain close to Martha, Lionel agreed, indicating how much he valued his relationship with Martha. Jonathan died protecting his family, which was the most important thing in his life.
Lionel told Martha he would help her through her grief and also convinced her to take Jonathan's seat as senator. Martha appreciated his help but was unable to trust him completely when she was blackmailed into paying a criminal to hand over a DVD exposing Clark's powers. Lionel could sense that Martha needed help and followed her to the drop off, scaring the blackmailer away. This angered Martha, as she was concerned what the fallout would be. Lionel calmed her and insisted that he would take care of it, which he did. Martha was incredibly thankful to Lionel, but nervous that he may have watched the DVD. He assured her that he had no hidden agenda and was only interested in helping her. He then pointed out the risks that come with being a senetor, which were made greater by any involvement with him. His graciousness won Martha's trust and she told him that she wouldn't turn her back on her friends because of what people think. This pleased Lionel, although it became clear that he was merely manipulating Martha, as he had a copy of the DVD and knew about Clark's secret.
After winning Martha's trust they became closer and he took an interest in her professional development. He made an effort to attend her press conference after which he congratulated her on her success. He then offered to accompany her to an important dinner to help her meet the other senators. Martha could sense Lionel's growing feelings and warned him not to expect anything other than friendship, as she was clearly still recovering from the loss of her husband. Nevertheless, she agreed to go to the dinner with him, which worried Clark after he had a near-death experience and was warned by Jonathan's ghost that Lionel knew his secret. During Clark's near-death experience, Jonathan also requested that Clark keep Martha safe from Lionel, as he was clearly concerned by their growing relationship.
When Clark told Martha that Lionel knew his secret, she was nervous and blamed herself for getting his help with dealing with the blackmailer. She agreed with Clark to maintain a friendly relationship until Lionel's motives became clear. However, they were forced to confront this situation when disgruntled shareholder, Lincoln Cole, kidnapped Lionel and set up a string of tests that he had to pass to survive, including saving Martha from drowning, as Lincoln was aware of Martha and Lionel's growing relationship and wanted to use her to prove his disloyalty. Martha was locked in a tank that started to fill with water and Lionel had to find a hidden meaning in the sign; "a Toad like Fever" or Martha would drown. They desperately tried to communicate through the glass and eventually worked out that it was an anagram of "Failed Takeover", which Lionel understood to connect to Apex. As Lionel worked out the puzzle, the tank shattered just in time to save Martha's life. Martha then questioned Lionel's involvement in Apex and discovered the Luthor family disfunction. Martha then realized the differences between Lionel and Jonathan, as Lionel would rather resort to manipulation than sit down and have a father-son conversation with Lex like Jonathan used to with Clark.
Martha and Lionel then had to face Cole's final test where one of them had to shoot the other and if they didn't, their elevator cable would snap, killing them both. Lionel offered to sacrifice his own life and gave Martha the gun. Distraught at the prospect of killing her friend she couldn't do it. Lionel then took the gun and thinking that he was about to turn on her she gave a look of horror. However, to her shock Lionel went to shoot himself but discovered that the gun was empty. Cole admitted that he never intended to let them live. Lionel then selflessly pleaded for Martha's life, indicating how much he cared for her. Nevertheless, Cole blew up the elevator cables and it plummeted down the building, but Clark saved Martha and Lionel just in time.
Clark remained suspicious of Lionel and warned Martha, but she insisted that she saw how selfless Lionel could be. Both agreed that they had no choice but to trust him with Clark's secret. Nevertheless, Clark warned Lionel away from his mother, "secret or no secret", although Lionel's bond with Martha was stronger than Clark anticipated, as they remained in contact. Clark's distrust of Lionel was fueled when Brainiac, posing as Jonathan, told him to kill Lionel due to a dangerous weapon that he had. Thinking that his father was giving him a message from beyond the grave, Clark confided in Martha. She was initially sceptical, choosing to trust Lionel. However, Brainiac then went to speak to her disguised as Jonathan as well. He questioned her relationship with Lionel, but she insisted that they were only friends and that she truly missed him. He then told Martha that Lionel was dangerous and must be eliminated and alluded to Lionel being responsible for his own death. This shocked Martha and put doubt in her mind about Lionel's true motives, but when she pressed him for more details, the apparition disappeared.
After discovering that Clark knew that he had spoken to Jonathan before he died, Lionel went to confess to Martha. He explained that he told Jonathan that he knew Clark's secret but it made him so angry that he didn't let him explain. Martha was clearly shocked and disappointed. She was unable to reply so Lionel left saying that at least he was honest.
Lionel tried to make amends by offering Martha transportation to her meeting. She accepted and during the flight Lois mentioned the many favors that Lionel had been offering Martha. She questioned if Martha had feelings for him but she was still insistent that they were merely friends.
Martha and Lionel were glad to find each other during Dark Thursday. They supported each other as they faced the prospect of killing General Zod with the Kryptonian dagger, yet Clark ultimately defeated Zod. After this, Lionel claimed to have lost his connection with Jor-El. It soon became apparent that Lionel was being dishonest with Martha and Clark, as he continued to write Kryptonian symbols.
Having seemingly forgiven him for his involvement in Jonathan's death, Martha continued her relationship with Lionel and attended a fundraiser as his date. He even loaned her an expensive necklace. However, Lionel soon got cold feet about their growing relationship and told Martha that he would not come to Thanksgiving dinner. This provoked a discussion about what was happening between them. Lionel impulsively leaned in to kiss her, much to Martha's surprise. Embarrassed, he left abruptly. Later, Martha went to Lionel's office to reassure him that she still wanted him to come for Thanksgiving. While she admitted that she knew that there was something between them, she made it clear that she was not ready to figure out what it was. Nevertheless, she valued their friendship and saw no reason for it not to continue. Lionel then agreed to join her for dinner, prioritising Martha over his son.
Martha visited Lionel in hospital after he was badly injured during an explosion, showing deep concern for Lionel. After Lionel forced Lana to marry Lex by threatening to kill Clark, Lana used Lionel's weakened state to her advantage. Aware of his close relationship with Martha, Lana threatened to tell her about Lionel's threat but Lionel kept quiet indicating that, despite his love for Martha, he would put Clark's safety before her, which surprised Lana. Martha later admitted to Clark that she didn't completely trust Lionel, as she was reluctant to believe someone could completely change. Nevertheless, she was keen to give him a chance.
Lionel suggested to Martha that she take over for Senator Ed Burke in the US Senate until the next election. Putting Martha's needs before his own, Lionel endorsed her taking the position, even though she had to move to Washington DC. He wished her good luck over the phone while she was on her way explaining that he had faith in her.
Lionel kept in touch with Martha, despite her move to Washington and phoned her to tell her how very proud he was of the work she was doing in the Senate. Despite their close relationship, Martha was not able to attend Lionel's funeral, as Lex blocked it off from any guests.
It is revealed by Clark that Martha inherited the Kryptonian library from Lionel after he was killed.