The purpose of this study was to extend previous research on the conditions that may promote understanding and abstraction via structural alignment, that is, through a comparison between two partially understood situations. Structural alignment is a route to analogical reasoning which differs from the typical route where an analogy is made by eliciting an unknown situation from a very familiar one. Ninety-nine eighth graders were presented with two pairs of scenarios; the first depicting two phenomena of heat flow and the second, two phenomena of the changing state of matter. Participants were randomly assigned to five different conditions which varied in the degree to which they required a comparison between the phenomena in the scenario pairs. For each pair of scenarios, participants were asked to describe the differences between the two phenomena, explain what happens in the phenomena, rate the similarity between the two, and justify the ratings. Results show that analogical reasoning was promoted more in the condition where participants were asked to jointly interpret the phenomena depicted in the scenarios. For both pairs of scenarios, students in this condition reached a deeper understanding; they were more able to identify alignable differences between the phenomena, and recognize the abstract and general higher-order relational structure implied by the perceptually different situations.