Background: Team-based instructional change is a promising model for improving undergraduate STEM instruction. Teams are more likely to produce sustainable, innovative, and high-quality outcomes than individuals working alone. However, teams also tend to involve higher risks of failure and can result in inefficient allocation of valuable resources. At this point, there is limited knowledge of how teams in the context of STEM higher education should work to achieve desirable outcomes. Results: In this study, we collect semi-structured interview data from 23 team members from a total of 4 teams at 3 institutions across the USA. We analyze the results using a grounded theory approach and connect them to the existing literature. This study builds upon the first part of our work that developed a model of team inputs that lead to team outcomes. In this part, we identify the mechanisms by which input characteristics influence teamwork and outcomes. Team member data expand this initial model by identifying key aspects of team processes and emergent states. In this paper, we present five team processes: "strategic leadership," "egalitarian power dynamics," "team member commitment," "effective communication," and "clear decision-making processes," that shape how teams work together, and three emergent states: "shared vision," "psychological safety," and "team cohesion," that team members perceived as important aspects of how teams feel and think when working together. Conclusions: This work furthers our understanding of how instructional change teams can be successful. However, due to the highly complex nature of teams, further investigation with more teams is required to test and enrich the emerging theory.