You are right, there are two points in space-time (the definition of the word "event" in special relativity). But the "space time distance" between them is zero! (another way to say that is that the two points have light-like separation)

All of the weirdness of special relativity stems from that definition of "space time distance", which is just an extension of Pythagoras' theorem:

distance = sqrt(x^2+y^2+z^2-(c*t)^2)

x, y, and z are the differences in spacial coordinates between the two events (in a given coordinate system) and t is the difference in time coordinates (in the same coordinate system). The minus sign is where the interesting effects stem from.