Powering a DC motor with an external battery
Your schematic is bad - the motor is connected betveen base and power, emitor is connected to ground.That keeps the transistor open, and B-E voltage is like 0.7V, rest is for the motor to rotate.
More over the transistor is open, so if you send pulses from pin 3, they are shortcuted to ground thru the transistor, not affecting the motor at all.

Switch the wires to Base and to Colector (lines 48 and 49) and it should work better.

(Still I would not use divider 9->6 volts, losing a lot of power constantly, I would rather change the PWM little down (and have it relatively fast, 1kHz or more) and the motor should be OK, if effective voltage ther would be under 6V - so the PWM under like 66% HIGH. Also shortcutting pin3 to ground with resistor is not optimal, the resistor should be between pin3 and Base.)