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Teacher attrition rates are high in urban schools, particularly for new teachers and science and math teachers compared to other subjects (Ingersoll & May, 2012). Research indicates teachers who remain committed to teaching in high-need schools are unique; they tend to identify not just as teachers, but as teachers devoted to the mission of social justice and working with underserved students (Moore, 2008). Teacher education programs have an important role to play in the preparation of teachers within this social justice framework (Picower, 2012a). But, the transition from university preparation to in-service teaching is difficult (Beauchamp & Thomas, 2011), particularly for science teachers who encounter contradictory contexts in urban schools that undermine the pedagogical practices and mindsets learned in preparation (e.g. Rodriguez, 2015). However, little research has addressed how science teachers can be prepared to effectively bridge the divide between preparation and urban teaching. This dissertation utilizes the theoretical frameworks of identity (Gee, 2000) and agency (Archer, 2007) to address this gap in the literature. I employed a case study methodology of one cohort of four teachers from the Science Educators for Urban Schools (SEUS) program at Boston College, which serves as a critical case of an effective preparation program for urban science educators (Yin, 2013). Data, primarily interviews, surveys, and written reflections, were collected from study participants during preparation and their first year of teaching. The findings indicate the SEUS Scholars expressed a student-centered, inquiry-oriented approach to teaching science for social justice. While the SEUS Scholars struggled to implement their ideal science instruction as first year teachers given the contradictory contexts of urban schools, the social justice ideology of the pre-service program shaped their professional identity and feelings of agency. These findings illuminate the role of teacher preparation to support the development of: 1) a strong educational philosophy grounding their pedagogical approach to science teaching, and 2) pedagogical context knowledge to effectively navigate urban schools.