TH!NK is a new initiative at NC State University focused on enhancing students' higher-order cognitive skills. As part of this initiative, I explicitly emphasized critical and creative thinking in an existing bacteriophage discovery first-year research course. In addition to the typical activities associated with undergraduate research such as review of primary literature and writing research papers, another strategy employed to enhance students' critical thinking skills was the use of discipline-specific, real-world scenarios. This paper outlines a general "formula" for writing scenarios, as well as several specific scenarios created for the described course. I also present how embedding aspects of the scenarios in reviews of the primary literature enriched the activity. I assessed student gains in critical thinking skills using a pre-/posttest model of the Critical Thinking Assessment Test (CAT), developed by Tennessee Technological University. I observed a positive gain trend in most of the individual skills assessed in the CAT, with a statistically significant large effect on critical thinking skills overall in students in the test group. I also show that a higher level of critical thinking skills was demonstrated in research papers written by students who participated in the scenarios compared with similar students who did not participate in the scenario activities. The scenario strategy described here can be modified for use in biology and other STEM disciplines, as well as in diverse disciplines in the social sciences and humanities.