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- "Destiny? That's Jor-El talking! He did this to you -- I want my son back, give me back my son!" - Martha Kent (Crusade)
Martha saw Clark in the Smallville Hospital while reading to a comatose Jonathan. She took Clark home and showed him places to bring back his memory. However, he was "reprogrammed" by Jor-El and returned as Kal-El, with no knowledge of Clark's life and intent on fulfilling his destiny to reunite the Stones of Power. Martha was astonished when, out in the barnyard, Kal-El simply flew away. Martha contacted Virgil Swann, who sent his associate, Bridgette Crosby, along with a fragment of black kryptonite. When Martha exposed Kal-El to the fragment, Clark was able to overpower Kal-El and return to his normal self. Simultaneously, Jonathan awoke from his coma.
When Lionel switched bodies with Clark. Martha was shocked by the way Clark dressed and by his behavior and Clark/Lionel gave Martha a hug. Martha visits Lionel/Clark in prison and tells him she already knows that Lionel is in Clark's body. Martha along with Jonathan trick Lionel as Clark to go to the Cave so Clark can go back to his body and Lionel back in his.
Martha decided to run the Talon because by her working at the Talon it kept her mind off Jonathan's health: later on Martha hired Lois Lane as a waitress to work at the Talon. After Lois got kicked out of school Martha and the other Kents decide to let Lois live with them.
Jonathan and Martha were forced to leave Smallville because of another meteor shower heading for Smallville. Before they could leave, however, they were taken hostage by Jason Teague, who threatened to kill Martha unless Jonathan told him where Clark hid the Crystal of Knowledge However, Jonathan managed to attack him by surprise, but then a meteorite hit the Kents' house, partially destroying it. After the meteor shower, a disheveled Jonathan & Lois frantically search through the rubble for Martha. They find her unconscious, & take her to the hospital. Immediately after regaining consciousness, she asks Jonathan about Clark.