There are two important lines of inquiry.
I. Question-based.
i.e.
Whjat is the most important level to consider.
Who is causing this?
Who/what is supporting it/them?
Why are thy choosing to support them (if social science)
Some (many) believe pure scientists have no structured disciplined hierarchical methodology..
They believe even the "scientific method" cannot be contained in rules, that is just an idealization far from what actually leads to discovery.
II. Structure hierarchical methodology i.e. theory building, empirical research
1. Ontology. Domains can rely a on objective or non objective reality rules
2. Use of theory. One approach is one of theory with predictions. It uses postulates and mathematical basis of dynamics.
These are very sound. Still in social research there isunique requirements i.e. using tools, theoretical frameworks before methods because
3. Sound theoretical framework. Examples are the use competitive conflict in closed systems framework.
The power of mathematics and modelling is an alternative but sometimes one should have a sound theoretical framework based on tested domain-based principles of viewing reality - i.e. general principles of viewing reality is not always proper (most often not)
4. Method. A method that is used in science is hypothetico-deductive thinking (which has proven unyielding in domains related or close to the one under consideration, i,e., politics, social science)
Note:
Line of inquiry I is not asked by msinstream thinkers. They follow structured methodology and thus dont ask these questions.