In a study of the stop signal task (SST) we employed Bayesian modeling to compute the estimated likelihood of stop signal or P(Stop) trial by trial and identified regional processes of conflict anticipation and response slowing. A higher P(Stop) is associated with prolonged go trial reaction time (goRT)-a form of sequential effect-and reflects proactive control of motor response. However, some individuals do not demonstrate a sequential effect despite similar go and stop success (SS) rates. We posited that motor preparation may disrupt proactive control more in certain individuals than others. Specifically, the time interval between trial and go signal onset-the fore-period (FP)-varies across trials and a longer FP is associated with a higher level of motor preparation and shorter goRT. Greater motor preparatory activities may disrupt proactive control. To test this hypothesis, we compared brain activations and Granger causal connectivities of 81 adults who demonstrated a sequential effect (SEQ) and 35 who did not (nSEQ). SEQ and nSEQ did not differ in regional activations to conflict anticipation, motor preparation, goRT slowing or goRT speeding. In contrast, SEQ and nSEQ demonstrated different patterns of Granger causal connectivities. P(Stop) and FP activations shared reciprocal influence in SEQ but FP activities Granger caused P(Stop) activities unidirectionally in nSEQ, and FP activities Granger caused goRT speeding activities in nSEQ but not SEQ. These findings support the hypothesis that motor preparation disrupts proactive control in nSEQ and provide direct neural evidence for interactive go and stop processes.