I'm not quite sure what you're asking here, because the papacy rarely had any temporal power beyond the Papal States. The Papal States were a second-rate power at best, and rarely could project any kind of power outside their own borders. As you note, Pius VI was captured by Napoleon and the pontiff died in Valence, France and was not even afforded a Christian burial.

His successor, Pius VII, was able to turn the tables on Napoleon somewhat. Invited to Paris to be at the coronation of Napoleon as emperor, Pius VII accepted.

Pius's slow journey from Rome to Paris turned, without any planning or orchestration, into a triumphant procession. Enthusiastic crowds greeted the pope as he moved along his way, to Napoleon's great chagrin...Napoleon complained, "Nobody thought of the pope when he was in Rome. Nobody cared what he did. But my coronation and his appearance in Paris made him important." (A History of the Popes, John W. O'Malley, S.J., pg 236)

Pius VII's victory was short lived, as Napoleon once again occupied Rome and the pontiff was removed to France just like his predecessor was. Neither came anywhere near having the temporal power to greatly influence the course of events.