Tempered glass will not crack. It shatters into a million pieces. It broke when saw not anytime before.

How does the door operate in the opening. If you have to force it open causing it to flex, that's another possibility. Another avenue is extreme temperature changes from very cold to hot in a short time. This would be heightened if it is in direct sunlight where the space between the storm door and entry door heats up radically, quickly. The stone is definetely another possibility and would be my first guess as well. I've seen an auto side window with a chip shatter when the door was closed so your stone thought could very well be the case.

the front glass door on my parents home shattered in much the same way once. the door had settled out of square and you had to sort of pick up on it to open/close it. no one ever used that door, and it had gotten worse. when we went to open it one day to bring in furniture, it just shattered! turns out the door was torqued and when we opened the front door the glass door sucked in a little and the torqe put enough twist on it to shatter.

The inside pane of a sliding glass door shattered in our previous home, no one was home to see or hear it. I swapped the door out for a large window, saved the glass and built a garden shed with three large panes on the front roof. Looks really sharp and there was nothing wrong with the other three panes. No chips or holes.