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When Captain James T. Kirk set off for Qo'noS to find the traitor John Harrison, Marcus boarded his shuttle under the name Carol Wallace, using her mother's maiden name and claiming Admiral Marcus had assigned her. Spock deemed her credentials impressive but decided she was redundant, as he himself had been reinstated as first officer of the USS Enterprise. On the other hand, Kirk welcomed her aboard.

Spock confronted Marcus about her name not being in the ship's records, so Marcus apologized for the deception, explaining she had used her mother's maiden name to board the ship and examine the seventy-two experimental photon torpedoes her father had given Kirk to fire on Harrison. Spock informed Kirk about the deception, following Harrison's apprehension.

Marcus went with Leonard McCoy to examine a torpedo on a deserted meteor. McCoy accidentally activated the torpedo and trapped his hand, but despite Kirk's orders to beam her up, Marcus deactivated the torpedo before the emergency beam-up became necessary. Opening up the dormant torpedo, Marcus and McCoy discovered a cryogenically frozen man inside.

When questioned, Harrison revealed he was Khan Noonien Singh, revived to help prepare for war with the Klingon Empire, and that he had planned to smuggle his fellow Augments in the torpedoes before he was caught. Admiral Marcus appeared in the USS Vengeance, a warship designed by Khan, and began firing on the Enterprise. Carol Marcus revealed her presence to him in an effort to persuade her father to cease the attack, but he simply beamed her up and carried on. When taken to the bridge, Carol Marcus smacked her father but he ignored her, claiming the cover-up was necessary.

Scott deactivated the Vengeance's weaponry, giving Kirk and Khan time to fly to the ship and commandeer it. When they arrived on the bridge, Scott shot to stun Khan while Kirk admonished the admiral for compromising Starfleet. However, one shot was ineffective to keep Khan down, and he promptly beat Scott and Kirk. He then turned to Admiral Marcus, who tried to flee into the turbolift: Carol tried to stop him, but he responded by breaking her leg. Then he grabbed her father and crushed his skull before her very eyes, and she responded by screaming in horror.

Khan beamed Carol Marcus, along with Kirk and Scott, into the Enterprise's brig. Kirk brought her to sickbay for McCoy to patch her up. Khan resumed bombarding the Enterprise, and the damage caused the ship to fall to Earth. Kirk went into the warp core and reactivated the engines, preventing the Enterprise from crashing, but at the cost of poisoning himself. Marcus watched as Kirk's unconscious body was brought to sickbay. However, McCoy realized Khan's blood could be used to heal him. He and Marcus placed Kirk in one of the augments' cryotubes to put him in suspended animation. Spock and Uhura beamed down to apprehend Khan, after he crashed the Vengeance into San Francisco, and the blood transfusion proved successful.

Marcus attended a memorial for those killed by Khan and her father, close to a year later. She continued serving on the Enterprise bridge as science officer when it embarked on the first five-year mission.