Integrating science education with social justice is vital for preparing students to critically address significant societal issues like climate change and pandemics. This study examines the effectiveness of socioscientific system modeling as a tool within Justice-Centered Science Pedagogy (JCSP) to enhance middle school students' understanding of social justice science issues. It focuses on how system modeling can scaffold students' reasoning about complex social systems, informed by their lived experiences, cultural backgrounds, and social identities. Our research involved 27 middle school students using system models to explore the societal and scientific dimensions of the COVID-19 pandemic. By leveraging the experiences and insights of students, educators can create transformative learning environments that not only recognize but also utilize students' unique knowledge bases as legitimate contributions to classroom discourse. The implications for instructional design highlight the need for multifaceted, responsive activities that align with the principles of JCSP and empower students as agents of societal transformation. The research contributes to the ongoing discourse on enhancing science education through justice-centered approaches that address the complexities of socioscientific context and the cultural relevance of scientific knowledge.