The design of the m-Orchestrate learning system integrates mobile technology into the science curriculum, assessment, collaboration and inquiry-based pedagogy grounded in social constructivist theories with a more generic pedagogical structure as scaffolds for learners’ inquiry. The pedagogical structure is comprised of five elements: “engage, explore, analyze, explain and reflect” developed from the “inquiry-based learning model” in our earlier study, which will be employed in the design of inquiry phases in the m-Orchestrate-based learning. The use of these inquiry phases will serve for students’ achievement of knowledge integration through eliciting ideas, adding ideas, distinguishing among ideas and reflecting on ideas. In our system design, we modify the above five inquiry phases into “WeEngage, WeExplore, WeAnalyze, WeExplain, and WeReflect” to highlight the collaborative nature of the activities in m-Orchestrate.