This study investigates the effectiveness of using a learning module that combines interactive nonlinear storytelling games with three-dimensional (3D) simulation models. The story narrative is used to mimic real-world scenarios to train students to apply their knowledge. Using simulation software and games can facilitate practical understanding of complex systems and enhance students’ learning outcomes via situated learning. Situated learning is a pedagogical approach that places learners in real-life problem-solving situations to foster meaningful STEM learning. In this work, students use a nonlinear story to represent and express what they know about inventory and queueing models. Students use the simulation models to examine, analyze, and access virtual worlds that mimic real-world systems, interpret the information, organize their knowledge, and represent what they have learned. To investigate the effectiveness of combining nonlinear storytelling & simulation-based learning on students’ learning and motivation, two groups are compared: control (simulation-based only) (1), and intervention (nonlinear story and simulation learning game) (2). The control group is composed of students who used simulation models with a traditional case study format. In comparison, the nonlinear story and simulation learning game group is represented by the students who are taught with the aid of the game learning module. The results of this study compared the groups in terms of students’ motivation, engineering identity, and learning outcomes. The data of the control and intervention groups were collected in Fall 2020, and Fall 2021, respectively. The intervention group showed higher overall motivation and learning outcomes compared to the control group.