Solving organic chemistry reactions requires reasoning with multiple concepts and data (i.e., multivariate reasoning). However, studies have reported that organic chemistry students typically demonstrate univariate reasoning. Case comparisons, where students compare two or more tasks, have been reported to support students' multivariate reasoning. Using a case-comparison task, we explored students' multivariate reasoning. Our study was guided by the resources framework. One conceptual resource activates another conceptual resource and, successively, a set of conceptual resources. This successively activated set of resources is expressed in a line of reasoning. Pairing this framework with qualitative methods, we interviewed eleven second-semester organic chemistry students while they compared two substitution reaction mechanisms and chose the mechanism with the lower activation energy. We analysed what conceptual resources and lines of reasoning were activated and the variation to which students engaged in multivariate reasoning. Students activated multiple conceptual resources and, moreover, extended their activated resources into both developed and undeveloped lines of reasoning. When constructing their explanations, most students engaged in univariate reasoning. These students provided a developed line of reasoning selected from multiple activated resources, or they provided an undeveloped line of reasoning constructed from only one activated resource. Few students engaged in multivariate reasoning. These students provided both developed and undeveloped lines of reasoning from multiple activated resources. Our findings highlight the variation with which students engage in both univariate and multivariate reasoning. Therefore, we recommend that case-comparison activities scaffold engagement with multiple lines of reasoning in addition to activating and developing them.