Where, when, and how should we intervene on the School to Prison Pipeline (STPP)? Most scholars agree that there are many factors that influence the outcomes of youth that lead to incarceration, including, but not limited to: identity formation, peer effects, recidivism, and underachievement. Much of the literature has statically investigated these factors in isolation.However, despite the literature's emphasis on static models of isolated mechanisms, most scholars believe that the STPP persists due to an ecological system of interrelated factors that evolve dynamically (over time). What happens to human developmental trajectories when all of these mechanisms are at work simultaneously? And how might that inform where, when, and how we should intervene? This dissertation proposes a research paradigm that can eventually help answer these questions, presenting the first set of dynamic mathematical models that approach the STPP from a holistic, systems perspective. This perspective allows us to foresee surprising policy consequences that would not be obvious when analyzing these factors in isolated static models. It illuminates conditions under which small policy changes can lead to transformative, self-sustaining effects on school climate; large policy changes can have essentially no effect; and the same policy can have opposite effects under different initial conditions. This dissertation combines three interrelated studies, each focusing on a different subsystem within the STPP. The first is a macro-dynamic perspective of crime and arrest among youth, capturing the part of the STPP that exists outside of the school. Motivated by Study 1’s finding that biggest systemic contribution to the STPP is happening prior to the first arrest, the next two studies focus on parts of the STPP that exist inside the school. Study 2 focuses on how best to intervene on behavioral infractions through disciplinary policy. Finally, because achievement and positive academic identities are so preventive of antisocial behavior in schools, Study 3 focuses on underachievement and academic identity formation. This dissertation operationalizes an innovative research paradigm to dismantle the STPP, under the premise that reducing systemic disadvantage requires systems thinking.