I made a circuit which looks like this:
DO NOT connect the battery to the arduino like that.
Connecting the ground is not the problem.
You are connecting 9 volts to pin A3 - that will almost certainly damage the arduino.
Take a look at circuit 8A here. It's driving a relay coil but it will also work with a motor.
V+ is the positive terminal of the battery. The negative battery terminal goes to ground.
Of course, the transistor needs to be rated for the motor current (Amps or milliamps). Voltage is not a problem... Just about any transistor can handle 9V.
The diode protects the transistor and Arduino from the high voltage inductive kickback when the motor is turned-off.
The resistor prevents excess current from the Arduino into the transistor base (which could potentially damage either one, but is more likely to damage the Arduino).
When I built the circuit the first time I didn't use the A3 pin
You have no current limiting resistor from D13 to the base of the NPN. You were likely drawing way too much current from that pin, causing the Atmega processor to overheat. Sometimes they survive, sometimes they don't.
I'd replace the NPN with a logic level MOSFET; that's the easiest way to get this going. And don't forget the voltage divider on the A3 pin so you don't exceed the voltage rating of that pin.
Unless I have misunderstood your battery is the wrong way round. The long bar is positive, the short one negative. When I first learnt about electrical circuits I remembered this by imagining that I could cut the long bar in half and use the 2 pieces to make a + sign.
Plus everything everyone else said!
I like that one 
That always a bad sign, and a surprise if the Arduino continues to function.
Here is the usual circuit. You can substitute an NPN transistor for the MOSFET, but if you do, you might increase R2 to 470 Ohms.
The diode is required.
That's either CMOS latchup or you reversed the power and caused all the protection diodes to carry massive current - neither is good!
Or much better leave it as 180 ohms which is a better value for driving a motor. R1 is not needed for a BJT, but won't harm either.
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