The news on Wednesday night was breathtaking in its horror. One man had walked into the historic Emmanuel African Methodist Episcopal (AME) Church during Wednesday night prayer meeting — an institution at most traditional black churches — and after sitting with them for an hour, opened fire. He killed nine people, including the church’s pastor and state congressman Clementa Pinckney.

The shooter, twenty-one year old Dylann Roof, told the congregants that he had to shoot, claiming that black people were “raping our women and taking over the country, so you’ve got to go” as he reloaded his pistol. Roof echoed the false logic used to justify historic terrorist attacks on African American citizens — the lynching of thousands of black men, women, and children between 1890 and 1920, and days of terror at the hands of roving mobs of young white men during the Wilmington Race Riot of 1898 and the Atlanta Race Riot of 1906. For those who’ve insisted that this was anything other than race hatred, Roof’s evocation of the twisted language of historic massacres leaves no doubt.

In the days since, many, including President Obama, former Republican nominee for president, Mitt Romney, have said that the confederate flag — which is now literally chained to a pole in front of the South Carolina State House — should be taken down. In a dramatic turn around South Carolina’s governor, Nikki Haley, and South Carolina Senators Lindsey Graham and Tim Scott have reversed their positions in support of the confederate flag and asked the South Carolina legislature to pass a resolution removing it.

Others have insisted that we must move beyond symbolism and confront the workings of white supremacy. Citing the long history of violence targeted at Mother Emmanuel and other black churches, many are demanding that we understand this moment as part of history of domestic terrorism.

One thread in the conversation in the days following this attack is an implicit critique of prayer as an ineffectual response and the notion that the church is a point of vulnerability for black Americans. Hurt and angered by this act of terror, many have said that it is time to stop praying, insisting that prayer doesn’t work and that, by extension, the church isn’t an effective body through which to contest the hate that black people face today.

This discussion frames prayer and churchgoing as passivity. On the surface it makes sense — this unthinkable violence has caused so many in Charleston to pray publicly at the at the foot of Mother Emmanuel’s steps. The very pose of prayer — heads bowed, hands lifted in submission — looks like acquiescence.

However, this read masks the history of resistance that is at the heart of the black church in general and Emmanuel AME in particular. The roots of black Christianity are grounded in the fight for liberty. The independent prayers of the enslaved were seen as a fundamental threat to white supremacy in a society grounded in race slavery. The black church was a moral response to an immoral world and a space not only of faith but also independence and resistance, a space where generations of black leadership have emerged.

Founded in Philadelphia, Pennsylvania in 1819, the African Methodist Episcopal Church is the first independent black denomination in the United States. After decades of fighting for independence from mainline white Methodists, founders Richard Allen, Absalom Jones, and their congregants used the Christian faith as a means toward liberation. For them, faith wasn’t passive. Black Christians used faith as a cudgel against the institution of slavery.

Take the story of Allen, who became a Methodist during a revival in defiance of his “master.” Allen saw power in the idea that “in God all men are equal” and used his faith as an effective argument against his own enslavement, convincing his master to let him buy his own freedom.

Embracing the notion that “in Christ all are free,” the AME church would go on to be one of the most effective anti-slavery, pro-racial equality organizations in the nation. Its founding church, known as Mother Bethel, served as a safe haven for those who had run from the bonds of slavery. Congregants risked jail as they created hiding places and hid runaways, thwarting the efforts of slave catchers. Founder Absalom Jones, became the first black man to petition the Congress, presenting thousands of signatures as part of his active fight against the dangerous and unjust Fugitive Slave law. In a time when there were few schools for black people, Bethel served as a schoolhouse for both young and old.

Charleston’s Emmanuel AME was founded in the heart of the slave South with this same spirit of resistance. It was a congregation of both enslaved African Americans and free people of color, who first met in secret. Such meetings were dangerous for both. Advocates of slavery insisted that the supposed child-like nature of black folk rendered them incapable of surviving outside the bonds of slavery. The free people of Charleston disproved that, serving as an example to the enslaved about the possibility of liberty.

Through underground conversation, congregants linked their church to AME. Despite laws restricting free worship and even the reading of the Bible, free and enslaved alike began to bring their secretive worship to the surface and Emmanuel AME became the first church in the denomination south of Baltimore, Maryland. Soon thousands of congregants, enslaved and free, worshiped as members.

The church and its success was a threat to the logic of slavery. Rumors of a slave insurrection were traced back to Emmanuel AME and one of its founders, and free man of color, Denmark Vesey. Historians now debate if Vesey was a conspirator or falsely accused by local white slave owners who felt threatened by Vesey’s economic success and the church’s growing independence. Vesey was executed without confession during a secret trial, and the first Emmanuel AME sanctuary was burned to the ground in 1822. In the wake of its destruction, Charleston outlawed black churches altogether, pushing independent worship underground.

After the Civil War, Emmanuel re-emerged, rebuilt, and went on to be the heart of opposition to lynching, segregation, disfranchisement, and economic inequality. Risking the sanctuary once again, Emmanuel hosted Martin Luther King, Jr. and Wyatt T. Walker of the Southern Christian Leadership Conference for a rally on voting rights. Emmanuel opened its door again and again to be training ground for leadership.

It’s a shame that Emmanuel’s astute and outspoken pastor was first really in the national spotlight in the wake of his senseless death. Rev. Pinckney, and his willingness to lead in the fight against police brutality in Charleston symbolized the spirit of resistance at the heart of Emmanuel. I hope that today’s prayers will allow Emmanuel to rise again from the ashes and carry the legacy liberation we so desperately need today.