Distributed brain areas are engaged both during and following the elicitation of emotional experiences. Previous studies suggest that transient emotions may cause a prolonged impact (or inertia) on brain states, with corresponding changes in subjective affect and mood. To investigate the functional dynamics and reciprocal interactions among brain networks underlying these effects, we quantified co-activation patterns (CAPs) by recording functional magnetic resonance imaging (fMRI) during sad movies and subsequent resting periods. CAPs overlapping with the visual (VIS), default mode (DMN), central executive (CEN), and frontoparietal control (FPCN) networks showed not only distinctive effects of negative emotion on their spatiotemporal expression in both movie and rest periods, but also different reciprocal relationships among them in transitions from movie to rest. While FPCN and DMN expression increased during and after negative movies, respectively, FPCN occurrences during the movie predicted lower DMN and higher CEN expression during subsequent rest after neutral movies, but this relationship was reversed after negative movies. Changes in FPCN and DMN activity correlated with more negative subjective affect. These findings provide new insights into the functional dynamics and interactions of intrinsic brain networks, highlighting a major role of FPCN in emotion elicitation processes with prolonged impact on DMN activity in subsequent rest, presumably involved in emotion regulation and restoration of homeostatic balance after negative events.