Six years after the last Team X misson, Kayla and Logan lived happily together in the Canadian Rockies. She was seemingly killed by Victor Creed/Sabretooth after being stopped in her car. She dies before Logan was able to save her.
However, Kayla had actually survived her encounter with Sabretooth and reappears before Logan at Three Mile Island. She reveals that she faked her death in order to help release her sister Emma, which Stryker broke his promise to release her. Following the fight between Victor and Logan, Kayla said that she only did what Stryker wanted her to do because of her sister being held hostage. Logan and Kayla then proceed to free the mutant prisoners.
Kayla was shot by a guard when the mutants tried to escape. She told Emma to go without her and went to find Logan. After Logan was shot by Stryker with adamantium bullets, she dies after punishing Stryker with her abilities. Before Logan escapes the island, him and Gambit come across her lifeless body. Gambit asks Logan if he knows her. Unaware that he knows her due to Stryker shooting Logan in the head with adamantium bullets causing him to lose his memory, he says no. Logan shuts her eyelids before escaping the island.