The NPN has shown to be damaged if the Relay does not "click" and the motor of coarse run when wired on that way.
Ok, By understanding the power requirement AND the effort, the issue can be with the relay at 9V, how?
because the relay at 5V is 71.4mA average, and at 9V it jumps to 128.5 mA through the coil, in other words the Transistors Base current requirement goes from 8mA to needing 13 or so mA current.
What has most likely happened is the relay at 9 volt exceeded current for the transistors Base requirement somewhere,
and the Transistor went out.
The relay needs an current limiting resistor at 9V! an 50R resistor at 1/2 Watt, would bring the coil current back down to 74mA, close to the coils preferred current.
The Transistors Base was not getting adequate current at some point to drive the exceeding current from the relay and was not switched on enough for the then 128.5 mA, and the also possibility of the inductive flyback was not being sent to the power rail positive enough to remove the voltage spike completely. the relay flyback diode placed over the relay to the right hand side rail positive to help improve the removal of the relay switch off spike.
In most boards I have parted out, any diodes in the flyback arrangement were pointed towards the power Source, that should not have been needed here.
If the Transistor is replaced, then the relay would require the 50R in series with the coil from power supply, the Transistors Base can still use the 620R from the 555 pin 3 at 9 v supply.