One of the underlying themes purported by the movie is that the Vatican has entered into a conspiracy to suppress the "true words of Jesus" contained on the scroll of St. Thomas. Indeed, at the end of the movie there is a blurb that claims the Vatican has not recognized the scroll of St. Thomas. So, is there a conspiracy to keep the "words of Jesus" from us?
The crux of the matter lies in the scroll of St. Thomas itself. Indeed, in 1945 a historic find was made near the town of Nag Hammadi in Egypt. There, amid other ancient scrolls written near the time of Christ, was a scroll the movie Stigmata calls the scroll of St. Thomas, but is better known as the Gospel of Thomas.
According to the scroll itself, the contents are a compendium of many saying of Jesus, both proverbs and quotes. There is little narration, no story to read, just random quotes one after another.
Some of the quotes in the scroll appear to be authentic sayings-indeed, some are contained in the other four gospels in the Bible. Many of the other quotes, however, are unique to Thomas and seem quite antithetical and out of character to what Christ says elsewhere.
For instance, saying 85 reads, "Jesus said, 'Adam came from great power and great wealth, but he was not worthy of you. For had he been worthy, he would not have tasted death." Jesus is the last person we would expect to hear say that some could be "good enough" to never taste death.
So, if these sayings are purported to be the words of Jesus, why aren't they in the Bible? Well, for one, they were just discovered and the Bible has been considered "complete" for over 1,650 years and that's a lot of tradition to try and overcome. But secondly, there's no evidence that all these sayings are what they claim. Sure, the words of Jesus are quoted a number of times (at least, there are some sayings found in Thomas and in the four gospels in the Bible), but that doesn't necessarily mean all the sayings are from Jesus.
Very few scholars are willing to concede that the Gospel of Thomas is a legitimate gospel, nor that it was written by the apostle Thomas nor even anyone associated with the apostles. Instead, scholars believe the scroll was written by those who followed the gnostic form of Christianity and that many of the sayings were created or at least adapted to support their particular (and peculiar) beliefs.
So, is the Vatican conspiring to suppress the words of Jesus? Hardly. The Gospel of Thomas is widely available at most bookstores and is included in the Jesus' Seminars' work The Five Gospels. The movie Stigmata has obviously taken the fact that the Vatican has denied authenticity to the Gospel of Thomas and twisted that fact to try and discredit the Roman Catholic Church. But the reality is that Christian scholars of virtually every denomination and persuasion has denied authenticity of this as a legitimate gospel.
My advice? Save your money and go see something that with some credibility-like Star Wars part 12.