In 1043 Myra was overtaken by Muslims, and there was a fear that pilgrimage could become difficult and dangerous or that the shrine might even be desecrated. During this time, a group of merchants from Bari, a seaport in the kingdom of Naples situated on the Adriatic Gulf, sailed in three ships to the coast of Lycia (possibly under the request of the Pope of Rome) to obtain St. Nicholas' relics. They waited for an opportunity when none of the Muslim faithful were around and entered the church in which the relics were kept. They were met by a small community of monks who showed them were the relics were. The Barians told the monks why they were there, and the monks were adamant in their opposition. A confrontation ensued which resulted in the merchants taking the relics. After the Barians left the church, the monks told the inhabitants of Myra what happened, but they were too late to stop them before the merchants had made it safely aboard the ship. They landed at Bari on the 9th of May 1087, and the sacred relics were deposited in the Church of St. Stephen for safe keeping. From the first day the relics were in Bari, people were cured of various diseases.
I suppose it depends on who is telling the story if this was a good thing or not. If the merchants had not taken the body, would have the relics of Nicholas been desecrated? Was it the best thing that they be moved to Rome so that those in the West could venerate Saint Nicholas as well? Whatever the right thing to do was, Saint Nicholas now lies in Bari and a feast celebrates the transfer of his relics to Bari is held every May 9th. This is why sometimes people call him Nicholas of Bari.
A crypt for Saint Nicholas was completed by October 1089 and Pope Urban II laid the relics of Nicholas beneath the crypt's altar. The main church was finished ten years later, but sometime before 1197 (when it was officially consecrated) the Romanesque-style Basilica di San Nicola was complete, and now holds the relics of Saint Nicholas.
Oil is known to exude from Saint Nicholas's relics called "Manna of Saint Nicholas" and is used to anoint the sick. It was known to do this in the crypt in Myra as well as the crypt in Bari. Between 1954 and 1957 when the crypt was being renovated, the tomb was opened and the bones were exhumed. The relics were placed inside an urn and were visible for three years. The bones were observed to perspire and the linen sheet which held the relics was found to be soaking wet when the relics were re-interred in the tomb. And it still does this to this day.
When the bones were removed, a team of scientists was allowed to photograph and measure the contents of his crypt. In 2005, the measurements were sent to a forensics lab in England. It was revealed that he was barely five feet tall and had a broken nose (presumably from his imprisonment during the Diocletian persecution). Based on Saint Nicholas's skull, scientists have created a facial reconstruction showing what he may have looked like.
After the Reformation, Martin Luther tried to squash the celebration of Saint Nicholas day, when gifts were traditionally given. He didn't like the idea of saints and thought he day emphasized Saint Nicholas too much, rather than the true focus; Jesus. He introduced the idea of the Christ Child (or Christkindl in German) who would bring gifts on Christmas Eve when kids weren't looking. When the Puritans and the Anabaptists came to America, they wanted nothing to do with it, so they outlawed Christmas and kept it as a work day. In fact, Congress was in session the first Christmas under America's new constitution and Christmas wasn't declared a federal holiday until June 26, 1870. So the first "War on Christmas" was less about being able to say, "Merry Christmas", and more about not saying it all.
Later Germans would bring the Christkindl to America and the Christmas Eve gift-giving tradition and the Dutch would bring Sinterklaas. Sinterklaas is a contracted form of Saint Nicholas, and would become Santa Claus. Christkindl would be corrupted in English to Kris Kringle, which is the "real name" of Santa Claus. Mix it all together with a bit of Americana and you get Christmas as we know it today.
Despite all the changes over the last hundred years, Saint Nicholas is still here, though some have forgotten, doing what Luther claimed he wasn't:
Pointing to Jesus.