Plasma transport during continuous extinction processes from high-current arcs to full extinction is an important issue in the study of vacuum arcs. However, to describe this transition, the traditional methods, magneto hydrodynamics or particle-in-cell, are limited by either accuracy or efficiency. In this paper, we developed a fully 3D hybrid plasma simulation algorithm to study the extinction process of multiple cathode spots in a vacuum environment. Cathode spots are modelled as independent plasma sources rather than treating the whole cathode surface as an indivisible source. For a better balance between efficiency and accuracy, ions are modelled as particles and electrons are treated as a massless fluid. Using this model, the effects of cut-off time and the locations of cathode spots on the extinction process are studied. The results show that during an extinction process, the total number of ions between the electrodes gradually decreases and the mean velocity of the ions gradually increases. When the current approaches zero, two regions can be observed in the gap: the separated jet region, and the common plasma channel region. The last three surviving cathode spots have significant impacts on the ion distribution at current zero, whose values depend on the distances to them. The closer together the three cathode spots are, the higher the value that the local ion density will reach. In addition, at current zero, the maximum ion density appears near the last extinguished cathode spot.