It literally means a pursuit of knowledge, investigation, or mode of prosecuting such an inquiry, or system. Currently, it more often means a prescribed process for completing a task.
If it refers to scientific method, it means a series of steps taken to acquire knowledge. It involves careful observation, skepticism about what one observes, formulating hypotheses, experimental testing and measurement of deductions, and refinement (or elimination) of the hypotheses based on the experimental findings.
If it refers to methodology, it means a comparison or study and critique of individual methods that are used in a given discipline or field of inquiry. It is the systematic, theoretical analysis of the methods applied to a field of study.