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Science learning is an important part of the K-12 educational experience, as well as in the lives of students. This study considered students’ science learning as they engaged in the instruction of scientific issues with social relevance. With classroom environments radically changing during the COVID-19 pandemic, our study adapted to teachers and students as they were forced to change from more traditional, in-person instructional settings to virtual, online instruction settings. In the present study, we considered science learning during a scaffold-facilitated process, where secondary students evaluated the connections between lines of scientific evidence and alternative explanations about fossil fuels and climate change and gauged the plausibility of each explanation. Our investigation focused on the relations between students’ levels of evaluations, shifts in plausibility judgments, and knowledge gains, and examined whether there were differences in these relations between in-person classroom settings and virtual classroom settings. The results revealed that the indirect relational pathway linking higher levels of evaluation, plausibility shifts toward a more scientific stance, and greater knowledge gains was meaningful and more robust than the direct relational pathway linking higher levels of evaluation to greater knowledge gains. The results also showed no meaningful difference between the two instructional settings, suggesting the potential adaptiveness and effectiveness of properly-designed, scaffolded science instruction.