The Methodology chapter provides details on the approach you used to address the problem you specified in your problem statement.
It is often helpful to think of verbs that you used to describe the work. e.g.,
A common structure would briefly (1-2 sentences) restate the problem.
Then, have a list of steps up front, like the above.
After that, there would be a sub-section, one for each step in the list that provides details.
For the details, what is often needed is design rationale that provides reasons for the choices made in each step of the methodology. For example, why was a particular toolkit or language chosen? Why was the range of parameters for evaluation used? What alternatives were considered but discarded?
Where appropriate, the Methodology chapter can include details on how an evaluation was done (e.g., through experiments). Sometimes, such details would be in a different chapter, however.
In most cases, the results from evaluation (typically in the form of tables and charts) is a separate chapter and not part of the Methodology chapter.