An animal’s movements and internal state generate an “internal backdrop” of activity that is dynamically modulated. During behavior, this internal backdrop interacts with signals arising from incoming sensory stimuli and may have a substantial impact on task-related computations, like those underlying decision-making. To understand the joint effects of internal backdrop and task-imposed variables, we measured neural activity across the entire dorsal cortex of task-performing mice. We characterized internal backdrop using multiple measures of self-generated parameters including pupil diameter, whisking and body motion. Surprisingly, internal backdrop dominated neural activity across the entire cortex, dwarfing task-related variables and even sensory stimuli. Single neurons in frontal cortex were likewise dominated by internal backdrop. A linear model allowed us to account for multiple dimensions of internal backdrop and uncover hidden signatures of task-related activity. We show that complex, ongoing behavior fundamentally shapes neural activity throughout cortex and must be accounted for when studying decision-making.