The spring was said to have had healing powers and was later venerated by the Etruscans and, following them, by the Romans. By the 1st century BC by a Roman temple of Minerva occupied the spring site. (Minerva, the senior female of the Roman Trinity, was herself an Etruscan carry-over.)
The town was Christianized in fits and starts during the third century: Constantine had already legalized Christianity, but the word didn't really get out to the provinces very well, and several early preachers and bishops were killed by mobs of protesting pagans. Things eventually settled down, and the temple of Minerva, like its counterpart in Rome near the Pantheon, became the church of Santa Maria sopra Minerva. One of the area's many earthquakes at some point diverted the waters of the spring elsewhere.
Assisi came under Lombard rule in the seventh and eighth centuries and was destroyed by Charlemagne in 773 during his wars against Arian Christian states. Charlemagne rebuilt it almost immediately, and about the same time the Rocca d'Assisi fortress was built on the small peak in the center of the northern wall of the town. Once the fortress was in place, Assisi became one of the most important Christian strongholds in the area. This made it an important player in the long series of wars nominally between supporters of Papal and (Holy Roman) Imperial power that ensued. These wars, of course, were really just battles among local warlords who sought to take over their neighbors -- their families allied themselves with either the Papacy or the Empire merely to gain local leverage. Assisi became an independent commune in the 12th century and was thereafter involved in disputes and battles with nearby Perugia.
It was in one of these battles, around 1202, that young Giovanni Bernardone, called Francesco by his semi-Frenchified family, was captured and imprisoned. He was about 20 years old, and until that time he had led an indulged and even riotous life. He neglected his studies, and, according to the Catholic Encyclopedia, "No one loved pleasure more than Francis; he had a ready wit, sang merrily, delighted in fine clothes and showy display. Handsome, gay, gallant, and courteous, he soon became the prime favorite among the young nobles of Assisi, the foremost in every feat of arms, the leader of the civil revels, the very king of frolic." His father was one of the town's richest merchants, an international cloth merchant who had married a woman of the petty French nobility. Francis could have whatever he wanted, and, in the fashion of the times for scions of wealth and class, he could get away with almost anything. He was said to be openhanded, however, and especially was generous to the poor of the town.
His imprisonment apparently sobered him up. Or at least it made him ill, and he started to contemplate his own mortality.
He was soon released, recovered from his illness, and, thinking again of military glory, was on his way to join a muster of crusaders in Spoleto when he had a relapse in 1205. He started to have visions and dreams, gradually broke away from his raucous companions, and eventually became his own mystical legend. (The Catholic Encyclopedia version of his story, based on accounts by his earliest followers, is at http://www.newadvent.org/cathen/06221a.htm.)
Many, including his own father, thought that the strain if illness and imprisonment had driven him mad. He had (and still has) supporters and detractors within the Church (although his detractors are now usually more circumspect.) Modern psychologists tend to do modern psychology things with his story, but they and their theories and explanations also have their supporters and detractors.
Holy or mad, St. Francis and his female counterpart, Clare (Chiara) of Assisi, made Assisi the shrine it is today. (Her story, also from the Catholic Encyclopedia, is at http://www.newadvent.org/cathen/04004a.htm.) The great artists of the immediate succeeding centuries, who were commissioned to memorialize the two saints and decorate their Assisi churches made Assisi the art museum that it is today.
The Franciscan religious orders that Francis and Clare founded split into factions almost from the day that Francis died, October 3, 1226, and the most important split was over how to memorialize Francis. The bone of contention was the grand Basilica that was started within a few years of his death by one faction of his followers and supported by successive popes. There were those among Francis's earliest religious companions who decried the expenditures lavished on a building in honor of a man who preached poverty. Their opponents argued that building-fund collections and grants from outside the area were giving employment to the town's and the region's poor (not to mention further enriching the rich) -- it was an early "trickle down" economic theory. The church obviously got built, attracted further grants and commissions, brought in more visitors, and for the most part still supports the town. The dissenters went elsewhere to do poverty the way they saw fit. It should be noted that, years before he died, Francis himself left town with a few such dissenters as the cult that grew around his name expanded beyond his desires.
When Francis died his remains were taken for veneration to the small Church of St. George, now a part of the Monastery of St. Clare. He had asked to be buried in the local potters' field next to the town's place of execution, but other forces intervened. Pope Gregory IX canonized him on July 16, 1228, two and one half months shy of the second anniversary of the death of Francis, and laid the cornerstone of the Basilica of San Francesco the next day. The building project, spearheaded by Brother Elias (Elia da Cortona), the new head of the Franciscans, was completed in 1253. In 1230, Elias had secretly entombed the remains of Francis deep below the altar.
The short period of construction of the basilica, one of Italy's largest and foremost religious monuments, is often explained as a measure of the great love which the people of the time had for St. Francis. It certainly also reflected the fund-raising and organizational abilities of Elias and his zeal in promoting the Franciscan Order. By the mid-1400's pilgrims were flocking to Assisi from all parts of Europe and, almost without interruption until today, the walled medieval town and its grand basilica have been among the most visited of Christian shrines. Assisi has also been popular for non-religious reasons and especially for its importance in art history.
P.S.: Assisi and all of Umbria were historically part of the province of Tuscany. There was no "Umbria" as a distinct political unit until 1860 when the Papal States shrunk to within the walls of Rome and Umbria, the last part of the shrinkage, became a province in united Italy. It is the only Italian province with no seacoast -- it essentially drains inward toward the upper Tiber River. .
There are thousands of books and articles about Assisi, its history and it's saints. Rome bookstores can provide many of them in English and dozens of other languages, and an even wider selection is available in Assisi. All the online bookstores have many of titles.
The Internet is also loaded, but almost everything is short and repetitive. A Google search for "Francis" and "Assisi" and "Basilica" got about 8 thousand hits: http://www.google.com/search?num=100&hl=en&safe=off&client=googlet&q=%2BAssisi+%2BFrancis+%2Bbasilica&btnG=Google+Search
There are lots of good Internet starting points in these thousands of links. Try http://www.assisi.com/index.php, and
http://www.assisiweb.com/ (this last, in Italian).
For Art in the Basilica, go to http://www.christusrex.org/www1/francis/francis2.html,
but remember that attribution of manyof the frescoes said to be by Giotto
are currently under serious dispute.