Carol Danvers, aka Captain Marvel, has been through her fair share of tumultuous situations in the comics. In Avengers Annual #10, Danvers has a run-in with Rogue, who steals her powers and leaves Carol in a coma. In Avengers #200, Marcus, a man claiming to be the son of Kang the Conqueror, kidnaps Captain Marvel, leaving her unable to trust the other Avengers. But in 2006's crossover event Civil War II, Carol hit the biggest obstacle in her comics career. Why? Because this time she was the bad guy.
Civil War II deals with the dangers of precognition, and what can happen to those who behave as if their presumptions about where society is headed are actual fact. A character named Ulysses Cain is the catalyst for Marvel’s second civil war, with his Inhuman powers allowing him to see the future. While Tony Stark is skeptical about acting upon Cain’s visions of the future, Captain Marvel isn’t quite so hesitant. Danvers puts together a small team to eliminate any threats that may arise as per Ulysses’ visions, and in doing so she becomes responsible for the casualties that follow, including Iron Man’s close friend James “Rhodey” Rhodes, or War Machine. Not only was Tony Stark ultimately killed by Carol in this story, but the ethical dilemma behind punishing someone before any crime had been committed led to conflict within the Marvel Universe for which Danvers was entirely responsible.
Captain Marvel unilaterally enforcing justice based on the unverified visions of a single civilian was a bad look, and one that didn't match with how Marvel had portrayed her character over the years leading up to Civil War II. In The Life of Captain Marvel, fans are given a coherent origin story of the character revealing her rise to accepting the responsibilities of a superhero, while earlier crossover House of M revealed that Captain Marvel wanted to move away from her establishment connections to become a more classic kind of superhero. Civil War II was a backslide for Captain Marvel from what fans have seen from her in the past in terms of her heroism, turning her into a stalwart authoritarian who was literally depicted arresting civilians without evidence - someone intent on control over service.
While Captain Marvel wasn't alone in her crusade during Civil War II, she is the driving force behind lax decision-making, which yields dire consequences for those she claims to care for. More damning, while Captain America was on her side during the conflict, he was later revealed to have been mind-controlled by HYDRA, meaning that retrospect didn't just rob Captain Marvel of her most important supporter, but rather revealed she'd been standing shoulder to shoulder with a terrifying villain. Over the course of Civil War II, Carol imprisons people who show no signs of guilt and even instigates a confrontation with Bruce Banner that leads to the scientist's murder by Hawkeye, who had been assured he would transform into the Hulk. Through it all, she remains resolute, claiming the ends justify the means even as they require her to go to war with half the hero community.
The ending of Civil War II doesn’t do Captain Marvel any favors either, showing that she is completely unrepentant and willing to accept higher authority, even after she won the conflict by accidentally killing Tony Stark. Civil War II showed Captain Marvel dealing in absolutes while fighting a war against friends that ultimately ended with her precious Inhuman ally ascending to another plane of existence, leaving two founding Avengers dead for the right to use an immoral advantage that was instantly lost. Since Civil War II, Marvel have put a lot of work into redeeming Captain Marvel, but since the story depicted her own considered decisions - and no get out like mind control or demonic possession has been offered - many fans have taken a long, long time to come back around to Carol.