Concurrently, Carol worked as a magazine editor and freelance writer in New York City. After working several cases with the Avengers, Ms. Marvel was invited to join the team during the Scarlet Witch's leave of absence. She quickly established herself as valuable member, but left the team following a bizarre unwanted pregnancy caused by 'Marcus', who claimed to be the son of Immortus. Marcus manipulated Carol into believing that she loved him and took her to his home in Limbo. However, Marcus' plot backfired when he discovered that he aged at an accelerated rate in Limbo. Eventually, Carol learned how to use Immortus' time-traveling devices and returned to her time.
Seeking peace of mind after the ordeal with Marcus, Carol relocated to San Francisco and chose not to resume ties with the Avengers. In a battle with the power-absorbing mutant named Rogue, Carol lost virtually all her Mr. Marvel abilities, leaving her with only her augmented genetic structure. After the fight, Rogue attempted to murder Carol by hurling her from the Golden Gate Bridge. However, Spider-Woman rescued Carol and alerted the Avengers and X-Men to Carol's plight. Rogue also drained her memories, most of which were restored by mutant mentor Charles Xavier. However, Professor X could not return the emotional bonds linked to those memories. During this period, Carol was a frequent ally of the X-Men -- Xavier's team of masked, mutant heroes.