As a precursor for investigation of changes in neural activity underlying lapses of responsiveness, we set up a system to simultaneously record functional magnetic resonance imaging (fMRI), eye-video, EOG, and continuous visuomotor response inside an MRI scanner. The BOLD fMRI signal was acquired during a novel 2-D tracking task in which participants (10 males, 10 females) were cued to either briefly stop tracking and close their eyes (Stop Close) or to briefly stop tracking (Stop) only. The onset and duration of eye-closure and stopping were identified post hoc from eye-video, EOG, and visuomotor response. fMRI data were analyzed using a general linear model (GLM) and tensorial independent component analysis (TICA). The GLM-based analysis identified predominantly increased blood oxygenation level dependent (BOLD) activity during eye-closure and stopping in multisensory areas, sensory-motor integration areas, and default-mode regions. Stopping during tracking elicited increased activity in visual processing areas, sensory-motor integration areas, and premotor areas. TICA separated the spatio-temporal pattern of activity into multiple task-related networks including the 1) occipito-medial frontal eye-movement network, 2) sensory areas, 3) left-lateralized visuomotor network, and 4) fronto-parietal visuomotor network, which were modulated differently by Stop Close and Stop. The results demonstrate the merits of using simultaneous fMRI, behavioral, and physiological recordings to investigate the mechanisms underlying complex human behaviors in the human brain. Furthermore, knowledge of widespread modulations in brain activity due to voluntary eye-closure or stopping during a continuous visuomotor task is important for studies of the brain mechanisms underlying involuntary behaviors, such as microsleeps and attention lapses, which are often accompanied by brief eye-closure and/or response failures.