Few people harbor as deep a hatred for Carol Danvers as the mutant shapeshifter called Mystique. When Raven Darkholme first appeared, she was working for a mysterious employer whose carefully-laid plans were somehow being disrupted by the activities of Ms. Marvel and Carol Danvers. Mystique became even more obsessed with destroying Carol Danvers when she learned from her precognitive partner, Destiny, that Danvers would cause her foster daughter, Rogue, immeasurable harm. Mystique vowed to prevent this, despite Destiny's warnings against it.
Over the next few months, Mystique systematically attempted to disrupt Danvers life. Eventually, she learned of Danvers' connection to psychiatrist, Michael Barnett. Mystique assumed Carol's form and visited Barnett's office. When she mistakenly greeted him as a lover would, Barnett realized that she was not Carol. Mystique proceeded to beat Dr. Barnett to death with her bare hands. She then stole his file on Carol Danvers. Within the file, she learned of Carol's dual identity as Ms. Marvel. When Carol investigated Dr. Barnett's murder, she uncovered Mystique as the culprit.
Through her preocognitive lover, Destiny, Raven was able to keep tabs on Ms. Marvel's life and activity. She ordered her Brotherhood of Evil Mutants to attack Carol, but they were easily beaten by the more experienced Ms. Marvel. Carol learned that it was Mystique who had ordered the attack and vowed revenge for this and Michael Barnett's murder. She did not have a chance to make good on her promise for revenge due to her abduction by Marcus. When Carol left Earth for Limbo, Mystique's plans for revenge were side-tracked.
Destiny sensed Carol's return months later but warned Mystique against contuning her plans to destory Danvers' life. Mystique's rantings about how she would not let Danvers harm Rogue was overheard by the young mutant villainess. Rogue decided that if Ms. Marvel posed a threat to her, she would be the one to deal with it. Rogue's unwarranted attack on Carol in San Francisco fulfilled Destiny's prediction when Rogue inadvertently absorbed Carol's mind and powers permanently.
Months later, Mystique and Carol's paths finally crossed when Carol and the X-Men infiltrated the Pentagon to erase the government's files on the mutant team. When they stumbled on Rogue in the hallway, an enraged Carol blew the X-Men's cover. Despite her anger, Carol allowed the X-Men to handle Rogue while she completed their mission. Carol was spotted by Mystique, who was there in her guise as Raven Darkholme. Unable to resist the opportunity to kill Danvers once and for all, Mystique pursued and shot Carol. Carol was only grazed and managed to defeat Mystique in unarmed combat. Mystique was apprehended and Carol successfully completed her mission. It is inevitable that these two will meet again now that Carol has returned to Earth and life as a super-hero.