In India, the Pala line was brought to an end in B.E. 1638 (1095 C.E.) by the anti-Buddhist Senas from the south. The Senas were Vaishnฺavite. They revived the orthodox Vaishnฺavism and supported the Tantric universities as institutions of learning and culture. The Sena kingdom of Bengal was short-lived; in B.E. 1742 (1199 C.E.) it was conquered by the Muslim Turks and Afghans. The fanatic invaders destroyed not only their political and military enemies, but all people and institutions of other faiths. Buddhist monks were mistaken as idolaters and cruelly murdered. All the shrines, monasteries, universities and schools were burnt and destroyed. At Nalanda the burning of the library continued for several months. Following are some passages from the book Tavakata recorded by the Muslim historian Minhazad:
"In the middle of the city there was a temple larger and firmer than the rest, which can be neither described nor painted. The Sultan thus wrote respecting it : 'If any should wish to construct a building equal to this, he would not be able to do it without expending an hundred thousand red dinars, and it would occupy two hundred years, even though the most experienced and able workmen were employed.' The Sultan gave orders that all the temples should be burnt with naphtha and fire, and levelled with the ground."

"Many of the inhabitants of the place fled and were scattered abroad. Many of them thus effected their escape. and those who did not fly were put to death. Islam or death was the alternative that Mahmud placed before the people."
"Most of the inhabitants of the place were brahmans with shaven heads (i.e., Buddhist monks). They were put to death. Large numbers of books were found there, and when the Muhammadans saw them, they called for some persons to explain their contents, but all the men had been killed."

"If they adopt our creed, well and good. If not, we put them to the sword. The Muhammadan forces began to kill and slaughter on the right and on the left unmercifully, throughout the impure land, for the sake of Islam and blood flowed in torrents. They plundered gold and silver to an extent greater than can be conceived. and an immense number of brilliant precious stones. They took captive a great number of handsome and elegant maidens, amounting to 20,000, and children of both sexes, more than the pen can enumerate."

"He fell upon the insurgents unawares, and captured them all, to the number of twelve thousand - men, women and children - whom he put to the sword. All their valleys and strongholds were overrun and cleared, and great booty captured. Thanks be to God for this victory of Islam."

"After wounding and killing beyond all measure, his hands and those of his friends became cold in counting the value of the plundered property. On the completion of his conquest he returned and promulgated accounts of the victories obtained for Islam, and every one, great and small, concurred in rejoicing over this result and thanking God."
So the monks who escaped death fled to Nepal and Tibet. With the destruction of the Sangha, the lay Buddhists were left without guidance. As there was then little distinction left between the theories and practices of the Buddhists and those of the non-Buddhists, the Buddhists were slowly absorbed in the non-Buddhist communities through the pressure of the Hindu caste system and the Muslim forceful conversion. Buddhist shrines which escaped destruction were turned into Hindu temples. Thus it was that Buddhism disappeared from India. Today only a few isolated groups of Buddhists remain in Bengal, Assam, Orissa and parts of South India. Buddhism is almost a foreign religion in the land of its birth.
The extinction of Buddhism from India at the time of the Turkish invasion led to a usual conclusion that Muslim persecution was the major cause of the disappearance of Buddhism from its homeland. Many even take it as support to a traditional charge that Islam is a religion of the sword which spread by the sword and was upheld by the sword. To confirm this, they quote from the Koran (Al-Qur'an):

"Prescribed for you is fighting, though it is hateful unto you" (2:212)
"O prophet ! Strive against the disbelievers and the hypocrites ! Be harsh with them. Their ultimate abode is Hell, a hapless journey's end." (9:73)

"O Prophet ! Exhort the believers to fight. If there be of you twenty steadfast, they shall overcome two hundred, and if there be of you a hundred steadfast, they shall overcome a thousand of those who disbelieve, because they are a folk without intelligence." (8:65)

"Truly, those who do not believe our verses we shall fry in the fire." (4:56)
"Fight them then that there should be no sedition, and that the religion may be wholly God's." (8:40)
"O ye who believe ! it is only the idolaters who are unclean; they shall not then approach the Sacred Mosque after this year." (9:28)