- "Clark, we're not trying to keep you from learning about your past. We just don't want to see you get hurt." - Martha Kent (Skinwalker)
Unharmed during the disastrous tornado storm, Martha volunteered at the Talon for the storm's victims, even as she worried over Jonathan and Clark's fates. When Clark resurfaced unharmed, she told him Jonathan was missing but tried to reassure him that it was not his fault. While helping out at the disaster relief, Martha remarked to Lana that the storm reminded her of the first meteor shower.
At the same time Clark developed heat vision, he was also at odds with Lex over Desirée Atkins and Martha stood up for her son, reminding him that Clark has been a good friend to Lex. Shortly after, Clark asked if he should tell Pete Ross his secret and Martha advised that Pete might not want the burden. When Clark told Pete anyway, Martha and Jonathan welcomed Pete with their family's biggest secret.
Clark provided another parenting obstacle when he was exposed to red kryptonite for the first time and inexplicably displayed rebellious and rude behavior. Martha and Jonathan were initially at a loss until they discovered the cause of the change. On a chance visit to the Luthor Mansion, Martha encountered Lionel Luthor, struggling with his new blindness. Lionel was so taken with Martha's personality, he offered her a job as his personal assistant. Martha admitted to Jonathan that she was very interested in the job.
Martha asked her father William Clark to help the farm's longstanding financial difficulties, but instead he arrived for an unexpected visit, Martha revealed that after a tumultuous relationship, she cut ties with him after she adopted Clark, believing that their history of disagreement would not stand the burden of Clark's secret. She found the key in Lionel's vault and hides it in the house, not even telling Clark or Jonathan about it.
She later quit her job after learning that he had a file on Clark in his office and her job caused to much conflict with her and Jonathan, another reason why she also quit that job working for Lionel. She and Lionel are kidnapped by an Insurgence team.
While finding hiding places for the key, Martha came in contact with spores containing the same materials as meteor rock and it almost killed her. However, the key was found and placed back into the Ship, as its light healed Martha and cured her illness.
When Clark destroyed the ship, the energy pulse caused Jonathan and Martha's truck to roll and she subsequently miscarried the baby. She was still in the hospital when, out of guilt, Clark dosed himself with red kryptonite and ran away. She spent the summer answering his silent phone calls, pleading for him to return home.