The goal of this research study has been to develop, implement, and evaluate a school reform design experiment at a continuation high school with low-income, low-performing underrepresented minority students. The complexity sciences served as a theoretical framework for this design experiment. Treating an innovative college preparatory program as a nested complex adaptive system within a larger complex adaptive system, the school, we used features of complex adaptive systems (equilibrium, emergence, self-organization, and feedback loops) as a framework to design a strategy for school reform. The goal was to create an environment for change by pulling the school far from equilibrium using a strategy we call “purposeful perturbations” to disrupt the stable state of the school in a purposeful way. Over the four years of the study, several tipping points were reached, and we developed agent-based simulation models that capture important dynamic properties of the reform at these points. The study draws upon complexity theory in multiple ways that have supported improved education for low-achieving students.