The changes you saw in the bag on a macroscopic scale are due to changes at the microscopic scale.
As the water moves from the cup and into the bottom of the sealed plastic bag, we are witnessing changes in matter and energy. On the first page, we determined that the energy source present here is the sun. The water in this demonstration is moving through 2 phases of the water cycle.
In order for matter to move, it must change state. The three major states of matter are solid, liquid and gas. The specific molecules here are present in liquid or gas form.
Think about what molecules of matter are moving, where are they moving to, and if there is matter that does not move.