Research suggests that students hold misconceptions about the immune system, but little is known about how they reason about the mechanisms by which the immune system operates. This study investigated how students reasoned about the immune system in Beirut, Lebanon. The study used a qualitative approach and investigated 16 Grade 12 participants who learned an immunology unit for one month. Data analysis was based on students' responses during a pre/post written assessment and one-on-one semi-structured post-unit interviews to determine the levels of reasoning. The results revealed misconceptions about different immune elements and identified five levels of reasoning. The first level of reasoning revealed responses of informal/ everyday nature. The second level of reasoning revealed responses identifying a simple mechanism of the non-specific immune response. The third level of reasoning involved responses identifying simple processes of the specific immune response. In the fourth level of reasoning, students' responses recognized complex immune mechanisms without relating the microscopic elements to the macroscopic response. Finally, in the fifth level of reasoning, students' responses identified the complex processes and linked micro-elements to macro observations. Our findings indicated that identifying the molecular structures and their roles is a stepping stone to understanding the immune system holistically. We explained how this study extends the literature on systemic reasoning and discussed those results by determining the difficulty of reaching the highest level, suggesting implications for curriculum and instruction.