Investigators have not made a final determination on the authenticity of the manifesto and photos but are working under the belief they're as real as they appear to be, a federal official briefed on the probe told ABC News.
They "don't have any indication that it isn't [authentic]," the source said. "We just can't make the definitive link."
The site allegedly revealed disturbing views about race in addition to dozens of photos believed to be of Roof, including one of him holding a gun and another of him holding a Confederate flag.
Towards the end of the purported manifesto, the writer explained why Charleston was chosen as a target.
“I chose Charleston because it is most historic city in my state, and at one time had the highest ratio of blacks to Whites in the country,” the writer said. “We have no skinheads, no real KKK, no one doing anything but talking on the internet. Well someone has to have the bravery to take it to the real world, and I guess that has to be me.”
Former FBI agent Michael German, who has infiltrated white supremacist groups, said the writer of the purported manifesto fits a pattern of an individual with a "deep-seeded hatred." He said those individuals often turn to the Internet and different groups "trying to find some justification where their anger and frustration can fit in."
Though Roof doesn't appear to be directly a part of a white supremacist group, German said it's not unusual for individuals to act alone.
"The above-ground groups, the groups you hear about, the so-called hate groups, tend not to be involved in criminal activity because they're identifiable, [so] it's easy to find them," he said. "There are individuals within the movement are actually instructed to go out and do something on their own or with a small group, a small cell of like-minded people."
Roof, 21, was apprehended in Shelby, North Carolina, about 250 miles from where he allegedly opened fire inside the Emanuel AME Church on Wednesday night at Bible study. He allegedly confessed to the killings, according to a law enforcement source briefed on the investigation, and has been charged with nine counts of murder and possession of a firearm during the commission of a violent crime.
ABC News legal analyst Dan Abrams said Roof's defense team may have difficulty pleading an insanity defense.
"The insanity defense is so hard to win, particularly in a case like this, where [there] seems to have been so much sort of premeditation and thought about how he was going to do what he was going to do and why he was going to do it," he said.
Ashley Pennington, a public defender assigned to Roof, has not responded to ABC News' request for comment.
“I forgive you,” the daughter of victim Ethel Lance, 70, said through tears to Roof, who appeared at the bond hearing via video-conferencing from jail. "You took something very precious from me and I will never talk to her ever again. I will never be able to hold her again. But I forgive you. And have mercy on your soul."
"We welcomed you Wednesday night in our bible study with open arms," said Felicia Sanders, the mother of 26-year-old Tywanza Sanders.
"Every fiber in my body hurts," Sanders added. "And I'll never be the same."
Alana Simmons, granddaughter of victim Daniel Simmons Sr., 74, said, "Although my grandfather and the other victims died at the hands of hate, this is proof everyone's plea for your soul is proof that they lived and loved and their legacies will live and love. So hate won't win and I just want to thank the court for making sure that hate doesn't win."