Mathematics education reform has led to more conceptually focused instruction in the classroom. Yet, students with disabilities are receiving fewer chances than other students to engage in meaningful mathematics. Furthermore, a research divide between mathematics education and special education in mathematics has led to significant gaps in research on the individual and conceptual understanding of students with disabilities. Through task-based interviews and classroom observations, this study begins the process of closing this research gap through an examination of students' understanding of variational and covariational reasoning. Data suggest that the participants, two students with disabilities, increased their conceptual understanding in a reformed learning environment with support from teacher presence and questions. The students were able to increase their understanding of the difference between discrete and continuous functions, demonstrated an ability to self-correct, and improved their ability to choose appropriate levels of reasoning. The results suggest that conceptually oriented instruction with the presence and questioning of a teacher can support students with disabilities in developing a deep and rich understanding of complex mathematics.