Among health behaviors, physical activity has the most extensive record of research using passive sensors. Control systems and other system dynamic approaches have long been considered applicable for understanding human behavior, but only recently has the technology provided the precise and intensive longitudinal data required for these analytic approaches. Although sensors provide intensive data on the patterns and variations of physical activity over time, the influences of these variations are often unmeasured. Health behavior theories provide an explanatory framework of the putative mediators of physical activity changes. Incorporating the intensive longitudinal measurement of these theoretical constructs is critical to improving the fit of control system model of physical activity and for advancing behavioral theory. Theory-based control models also provide guidance on the nature of the controllers which serve as the basis for just-in-time adaptive interventions based on these control system models.