Starting in 1968, Khalifa believed that he had discovered an intricate numerical pattern in the text of the Qur'an involving the number 19. The pattern involves counting of words and letters, and calculations involving the numerical equivalents of the letters. He published several books on this subject.
Khalifa was initially well-received, but became the subject of bitter controversy when he made several claims that appeared heretical according to the mainstream opinion of both the Sunnite and Shiite schools of thought.
Khalifa denounced two long-accepted verses (9:128-129) of the Qur'an as false additions, thus portraying himself as a "purifier" of the Qur'an. He justified this by means of his numerical patterns and also claimed to have discovered historical evidence that the verses had been incorrectly added to the Qur'an in the first place. In addition to doubting the alleged historical evidence, his critics noted that Khalifa had initially produced patterns that included the verses and only removed them (and made other lesser changes to the text) when errors were demonstrated.
The controversy surrounding Khalifa deepened when he used his patterns to declare himself as a messenger of God, alongside of Abraham and Muhammad. His claim of messengership caused him to be considered a heretic and an apostate by the main corpus of muslims. To justify his claim he put forth novel interpretations of the words "messenger" and "prophet" so that he could align his claim with a Quranic verse declaring Muhammad to be "the seal of the Prophets", usually taken to mean that Muhammed is the final prophet. Then he presented numerical patterns which wove those words together with the names of Abraham, Muhammad and his own name.
As stated, Khalifa rejected the importance of the sunnah and hadith in Islam. This has also caused the spawning of several groups with similar ideas yet unconnected with his main group.
Several muslims have published detailed refutations of Rashad Khalifa's numerical patterns, and a large literature opposes his theological innovations. The controversy continues.
On January 31, 1990, Khalifa was stabbed to death in his Tuscon mosque. It is commonly believed that an extremist group al-Fuqra based in Pakistan was responsible, but it is unclear whether this has been positively established.
Controversy on denouncing verses in the Qur'an
Controversy on claim of messengership
Controversy on hadith and sunnah