A methodology chapter is particularly important for a thesis that discusses primary research that the student conducted, because it lets the reader know the manner in which the student progressed. Later, knowing that manner allows the reader to attempt to reproduce the student's results or to accept or deny their accuracy.
The methodology chapter should describe the student's research methods in detail, including any element whatsoever that may have affected the research results. For example, if the student conducted a series of experiments on seeds that large agricultural companies produced, he or she would need to specify the conditions under which the experiments ran, such as in Iowa in July or inside a greenhouse in western Idaho in the winter. To the trained eye, these details may have profound implications, because the environment may have dramatically affected the results of the experiment.
Methodology chapters should also describe any specific equipment that the student used to conduct primary research. The student should describe any tools or computer software developed during the course of the thesis project, as well as any purchased equipment whose presence in the research the reader may not have inferred easily. For example, the student in the agricultural example may not need to mention having used a spade and garden gloves, but he or she must mention a piece of equipment that measures the force of the sun's rays on the seeds.
In a thesis that explains primary research that the student conducted, the methodology chapter should usually come directly after the hypothesis chapter, in which the student states the idea that the experiment or research will test. In sequencing the chapters this way, the student will prepare the reader to accept the results of research as openly as possible; he or she will have expressed the idea under exploration as well as the equipment that does the exploring, and the reader will view the findings with a serious consideration to those preliminary matters.