CHARLESTON, SC – (CNN) Of the thousands of services in the church’s 199-year history, the one Sunday took on an added poignancy.

Behind the podium at Emanuel African Methodist Episcopal Church, a chair sat empty with a black cloak draped over it. It’s where the Rev. Clementa Pinckney would have been sitting, had a gunman not killed the pastor and eight other worshippers at a Bible study Wednesday night.

But instead of just pain, hymns and gratitude also filled the church in Charleston, South Carolina.

“The doors of the church are open,” the Rev. Norvel Goff declared. “No evildoer, no demon in hell or on Earth can close the doors of God’s church.”

As nine families continue grappling with their loss, new developments are emerging on the investigation and the debate over what many deem a public symbol of racism.

The investigation

Dylann Roof told investigators he killed the nine worshipers at the historically black church because he wanted to start a race war, an official said.

Now, investigators are looking into a website registered to Roof, which features a 2,000-word racist manifesto that details the writer’s philosophy of white superiority.

The author said he “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 website, called the Last Rhodesian, is bare bones. Roof’s name doesn’t appear anywhere on the site, but he is shown in many of the photos. Some photos show him burning and spitting on an American flag or holding a Confederate flag.

On Friday, Roof appeared at a bond hearing. Families of the victims addressed him and did something many didn’t expect: they said they forgave him.

“I’m reminded of some news media persons that wondered why the nine families all spoke of forgiveness and didn’t have malice in their heart,” Goff said during the Sunday church service. “It’s that the nine families got it.”

And if the gunman was trying to start a race war, he failed.

“Lots of folks expected us to do something strange and break out in a riot,” Goff said.

“Well, they just don’t know us,” he said, as the congregation stood and cheered.

The flag

The Charleston massacre has reignited debate over whether the Confederate flag should keep flying over the state capitol in Columbia.

Protesters spanning all ages and races filled the front grounds of the state Capitol over the weekend, calling for the Confederate flag to be removed.

“Take it down, take it down,” the crowd chanted.

The dilemma of what to do with the Confederate battle flag — a symbol of racism to many and of Southern heritage for others — has flustered lawmakers for years.

As part of a compromise in 2000, lawmakers agreed to remove the Confederate flag from the top of the Capitol dome and place it across the street while also adding a monument to African-Americans. But the legislation mandated that only a supermajority of the legislature could change that set-up going forward.

Republican state Rep. Doug Brannon has already committed to introducing a bill to remove the flag when the legislature convenes in January.

“Personally, I have believed for years it needed to be in a museum,” Brannon told CNN’s Poppy Harlow on Sunday. “I apologize to the people of South Carolina. I’ve been in the House for five years. I should have introduced this bill five years ago.”

Asked why he didn’t file a bill before, Brannon replied: “I didn’t do my job.”

The unity

Outside the church Sunday, overflow crowds gathered in the street and listened to the service through loudspeakers.

When 3-year-old Cady Berardo saw the balloons at the makeshift memorial that covered the entire sidewalk, she thought it was someone’s birthday.

Her father, Alan Berardo, who was holding her in his arms, shook his head.

“This is a special church service,” he told her, “because four days ago a lot of people died here.”

“So we’re here today in church with God and everybody. Because we all have the same God,” he told his daughter.

At 10 a.m., churches around Charleston — nicknamed the Holy City because it has so many houses of worship — rang their bells in solidarity with Emanuel AME.

The bell at St. Matthew’s Lutheran Church rang 81 times — nine times for each victim.

The-CNN-Wire ™ & © 2015 Cable News Network, Inc., a Time Warner Company. All rights reserved. (PHOTO: LastRhodesian.com/CNN)