Conventional neuroimaging techniques suggest that attention and cognitive control result from interactions between different cortical areas depending upon the task. The time-course of these cortical interactions is critical to several previous models of how the brain controls the selection of attention and action. Recent methodological innovations now enable directly testing these hypotheses. I present recent data combining Transcranial Magnetic Stimulation (TMS) with electroencephalography (EEG) to explore what effect activity in a stimulated area has on activity in other areas and how this varies with the cognitive and perceptual state of the participant. TMS was applied to a control network of medial, frontal and parietal cortices, and also to early visual cortex, in order to delineate the patterns of functional connectivity underlying phosphene perception, visual priming, attentional control and the resolution of response conflict. The results not only show that specific cortico-cortico interactions are modulated during particular tasks, but also that TMS can be used to explore the neural dynamics underlying perception and action.