When we observe the Universe, we sometimes see things behaving in ways we can't explain or hadn't predicted. For example, when looking at galaxies, the speed they revolve at suggests that there should be more gravity than explained by what we see to hold them together (Section 3.2).  

In fact, astronomers now estimate that the stars, galaxies, planets, etc, make up only about 4% of the total mass in the Universe, and of this we can only actually "see" about 0.5% because of the light emitted by stars.

The rest is made up of matter and energy that we can't observe.  It does not absorb, reflect or emit light which makes it extremely difficult to detect.  We can only see what it is doing by the effects on gravity.  We call this 'dark matter' and 'dark energy'.

(credit: Hobby-Eberly Telescope Dark Energy Experiment)