The empirical Green's function method (eGf) is innovated to examine the rupture nucleation and propagation during the disastrous Athens earthquake of September 7, 1999 ( M L=5.4). Waveforms recorded at seven regional broadband stations are studied. One of the two strongest aftershocks ( M L=4) was selected as the eGf, but its focal mechanism differs from the mainshock mechanism. Therefore, the paper suggests an innovation of the classical eGf method. The assumption of the similarity of the mainshock and aftershock focal mechanisms is relaxed as follows: the mainshock is modeled by an eGf-like method using synthetic weak events, computed by discrete wave number method (DW), two times, once with the focal mechanism of the mainshock and again with the assumed focal mechanism of the aftershock. These computations are used to determine the subset of the stations at which the disparate focal mechanism results in a (station-dependent) multiplicative factor only, with minimum waveform distortion. Real data from that station subset are then inverted as if the mainshock and aftershock mechanisms were the same. The eGf synthetics are produced for constant-velocity radial rupture propagation starting at 36 trial grid points, regularly distributed on the fault plane, and the grid point providing the best fit to the observed waveforms is assumed to be the nucleation point. Synthetic tests show that success of the method strongly depends on the exact knowledge of the mainshock true fault-plane orientation, but that is fairly well known from the aftershocks distribution in this case. The aftershock sequence suggests two possible sizes of the fault: a large fault (20×16 km along strike and dip, respectively) and a small fault (8×10 km) that fills in the gap identified during the first 12 observation days between two aftershock clusters. The eGf modeling does not resolve a preferred fault dimension. However, for both sizes, the method locates the nucleation point at the western part of the fault plane, thus clearly indicating the rupture propagation toward Athens.