Model-based reasoning has been introduced as an authentic way of learning science, and many researchers have developed technological tools for learning with models. This paper describes how a model-based tool, "BioLogica"™, was used to facilitate genetics learning in secondary 3-level biology in Singapore. The research team co-designed two different pedagogical approaches with teachers, both of which involved learner-centered "exploration and reflection" with "BioLogica" and teacher-led "telling" or "consolidation." One group went through the stand-alone "BioLogica" units for all topics prior to a series of teacher-led instructions, whereas the other group was engaged in teacher-led activities after using "BioLogica" for each topic. Based on the results of a series of tests on genetics, the groups performed differently from what the teacher had expected. We explore how the design of the two approaches and interactions among students might have contributed to the results.