Transistor slows motor instead of turning it off
I can't make much sense of your diagram-  but this is the correct way to do it: 







simulate this circuit &ndash; Schematic created using CircuitLab

R1 is low enough that the base gets 10-15mA of drive, sufficient for a few hundred mA of motor current. D1 protects the transistor Q1 when it turns off (from the motor inductance). The emitter of the NPN transistor should be grounded and then the collector will either be near ground or at the 9V level depending on whether it is off or on. 

You may have damaged the transistor you are using (due to breaking it down in reverse across the E-B junction) so I would suggest proceeding with a new one. You didn't mention it, but it probably got quite warm.