When an object is thrown upward, its initial velocity is positive. After that, gravity reduces its vertical velocity little by little until the object stops for an instant at the highest point.
At the highest point, the vertical velocity is momentarily zero, but gravitational acceleration still points downward.
This idea matters because students often think gravity disappears at the top. Only the velocity is zero for an instant, not the acceleration.
The sign of vy tells the direction of motion at that moment. A positive value means the object is moving upward, a negative value means it is moving downward, and zero means it is momentarily stopped.
Notice that height y does not automatically tell the motion direction. An object can be at the same height while moving upward and while moving downward, but the velocity signs are different.
Vertical motion also appears in projectile motion. Later, when an object moves at an angle, the horizontal part is read as sideways motion, while the vertical part still follows the gravity equations from this lesson.
That is why free-fall motion is useful beyond this page. The vertical part of a thrown ball, a projectile, or water leaving a hose is still shaped by gravitational acceleration.