JetBlue’s flight 206 (JBU206) flight crew initiated a go-around while over runway 04R due to Hop-a-Jet flight 280 (HPJ280) taking off without a takeoff clearance from runway 09 at Boston Logan International Airport (BOS). Runways 04R and 09 at BOS are intersecting runways. The BOS tower controller had instructed the pilot of HPJ280 to line up and wait (LUAW) on runway 09 while JBU206 had been cleared to land on runway 04R. HPJ280’s flight crew read back the controller’s instructions to LUAW, however they began the takeoff-roll instead. The airport surface detection equipment, model X (ASDE-X) alerted, and the controller issued go-around instructions to JBU206. JBU206’s flight crew initiated a go-around while over runway 04R, prior to reaching the intersection with runway 09. The closest proximity between both airplanes occurred when JBU206 was about 30ft AGL during the landing flare, close to the point where both runways intersected, see figure 1. A video file taken by the occupant of the flight deck observer seat was provided to the NTSB and a screen capture from the video is shown in figure 2. Figure 1. Flight tracks of both JetBlue (JBU206) and Hop-a-Jet (HPJ280) with yellow circle indicating incursion area. Figure 2: Screen capture from jump-seat occupant’s video recording showing Lear 60 crossing runway centerline. The captain of HPJ280 said that they had received clearance to cross runway 4L on taxiway E, and then take taxiway Mike, to Runway 9. On taxiway M he said, “they had heard a clearance that seems to be Line Up and Wait." He further stated that “he probably responded to the clearance, but in his mind, they were cleared for takeoff.” He said they performed the takeoff at 18:55 local time, and during cruise they received a message from ATC providing them with a phone number to call upon landing. After landing at FXE, BOS tower told them that they had taken off without authorization and caused an airplane that had been cleared to land on runway 04 to execute a go-around, passing about 400' above them. The first officer of JBU206 was the pilot flying, and they were on the ILS runway 04R approach. The captain of JBU206 said they had been cleared to land and had completed the landing checklist. On the tower frequency, they heard that an aircraft had been given LUAW instructions. As they entered the flare after crossing the threshold of runway 04R, about 30 feet above the ground, he saw an airplane cross 04R on runway 09 from his left and going to the right but could not estimate how far away the airplane was.