Tower Controllers described an AMASS directed abort when a taxiing aircraft entered the runway without authorization. Flight crew also reported their aborted takeoff incident.

Narrative

I was working Local 1 and 2 (Runway 3/28R). I taxied Dash 8 into position on Runway 28R with traffic; a CRJ9; on 3 mile final. Advised him to be ready for immediate departure and traffic on final. I scanned Runway and cleared the Dash 8 for an immediate takeoff. As the Dash 8 was passing A2 Intersection the AMASS advised Runway 28R occupied. I observed a Trinidad on Runway 28R at Intersection A6 on center line. I calculated the the Dash 8's Speed and position and decided to abort his takeoff. I informed him of the traffic on runway and he came to a stop just past A4 then I sent the CRJ9 around. The Trinidad was confused and would not take directions from Ground and remained on runway center line still taxiing opposite direction toward the Dash 8 before he realized he had to exit or hit him. He stopped just in front of the Dash 8 at A5 and finally cleared the Runway. I had the Dash 8 exit at A6 and go back to Ground. He returned to gate and they removed the wheel's and had to replace brakes and grounded the plane.