Here is a basic outline of scientific theory which has nothing to do with spirituality or religion and illustrates where matter fits into the scheme of things.
Ordinary matter can be explained with a non phenomenological theory which describes the nature of matter through the standard model of particle physics and is based on quantum field theories.
This is supported by particle accelerator experiments.
The existence of dark matter and dark energy comes through their measurable effects, there is no direct physical evidence of their existence.
For dark matter the effects are rotation curves of galaxies, gravitational lensing and escape velocities of individual galaxies in galaxy clusters; for dark energy it is the acceleration of the expanding universe measured through calculating distances using type Ia supernovae.
The objective of science is to find a non-phenomenological theory for the nature of dark matter and dark energy defined by the red arrow in the diagram.