The Pope's of those days were highly political leaders. In Dante's Inferno, there are several Popes in hell. I am amazed that he got away with writing it when he did.
Phillip Le Bel, King of France at the time, sent an army against the pope. He imprisoned him but was eventually forced to release him. That Pope conveniently died shortly thereafter. The next Pope, Clement, was virtually appointed by Phillip and his chief minister, de Nougerat. They ended up moving the Papacy to France for about 70 years. They set about destroying the Templars, as both a threat to their power grab and as a potential source of funds for their wars. The Templars snuck their treasures out of the country, along with their fleet, just before the axe fell.
I hold with the tales of the Templars taking their wealth and secrets to Scotland and aiding Robert the Bruce. There are also intriguing stories of some of the early bucaneers in the next couple of centuries having uncanny similarities in their traditions to the Templars.
There is an interesting and well documented parallel in eastern history. The Chinese emperor outlawed the Shao Lin (of Kung Fu fame) monks. They went underground and formed secret societies which later became the Triads (tong), who controlled much of the trade and organized crime in China and Chinese communities for the next several centuries, right up to today.
I've really enjoyed the well researched fiction of Katherine Kurtz on the history and fate of the Templars. She has written several stories herself as well as editing a couple of really good short story compliations. Though all are fiction, and some quite fanciful, they offer a great background for getting the feeling and for finding a starting place to research the real history.