To understand, study edge cases
This seems obvious, but is often forgotten. When a system functions efficiently, its individual parts are hard to notice. If you want to understand how a system functions, what it is made of, how each part works, but you cannot easily disassemble it and have a look, you have to get out of the nominal regime and let each part function independently, as much as possible.
To understand subatomic particles in a nucleus, or to figure out the structure of atom, hit them hard with other particles and see what happens.
To understand free will, focus on the situations where the notion fails.
To understand consciousness, study altered states.
To understand mental health, study mental illness.
To understand anatomy, dissect cadavers.
To understand logical reasoning, study biases.
To understand evolution, study artificial selection.
To understand economics, study market failures.