The 2011-2012 unrest of Santorini (Thera) volcano (Aegean Sea, Greece) was associated with microseismicity confined to the Kameni Line (KL), a major tectonovolcanic lineament, and has been regarded as a single magmatic episode, produced by a spherical source derived from inversion of GPS data. However, such a source is a few kilometers away from the KL and cannot explain observed microseismicity. For this reason, we divided the unrest episode into five periods based on the fluctuations of seismicity and deformation rates and investigated the connection between seismicity and two spherical magmatic point sources for each period. Based on a new inversion algorithm and consistent GPS data, we recognized during the volcano unrest episode an unstable pattern of intrusions correlating with both the KL and Columbo Line (CL), a second major tectonovolcanic lineament. Intrusions correlating with CL appear relatively persistent, aseismic, small, and shallow, which is consistent with marine geophysical evidence for arrested shallow dykes and geodetic evidence from a previous inflation episode. During the two periods of intense seismicity, sources close to the KL, explaining seismicity, were obtained. This unstable pattern of intrusions explains both the well-observed location and timing of seismicity as well as ground deformation and is consistent with results of an Okada-type inversion for a sill and a dyke. The stress interactions between the two sources agree with Coulomb failure stress models. Santorini appears to be affected by concurrent offset magma pulses, and only recent activity from a magma pulse below the KL produced microseismic swarms.