"and be carry’d into the Inquisition"
was introduced by Pope Gregory IX in the 1230s to suppress heresy. Victims were held captive, interrogated and often tortured before being put to death, if they opposed the Catholic Church.
In Defoe's time, the Tribunal of the Holy Office of the Inquisition, better known as the "Spanish Inquisition" was at its height. It was not formally abolished until 1834.