Although much research exists of students' alternative conceptions about evolution and natural selection, the way in which these vary in time and how scientific explanations change during instruction remains to be described and understood. Therefore, the main objective of this research is to characterise the nature of the change in student thinking about evolution through the mechanism of natural selection during a six-lesson intervention with a group of ninth-grade students (14-15 years old) from a private subsidised school in Chile. The study group included thirteen students to whom a pre- and post-test was applied using the questionnaire Assessment of Contextual Reasoning about Natural Selection (ACORNS), and from whom short tasks were collected at the end of three lessons. The data were analysed using a quantitative and qualitative analysis of nine students grouped in five cases of study. The main patterns described here are the recurrence of the design teleology thinking in students, the initial use of key concepts such as mutation, survival, and differential reproduction during the trajectories, the abundance of mixed thinking during and at the end of the instruction, and the low coherence in the structure of thinking, both in time and through the different contexts analysed.