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The Aryan invasion appears to have had a particularly devastating effect on Harappa. 

Despite the level of damage done to the archaeological site, human skeletal remains have been found  demonstrating some of the highest rates of injury (15.5%) found in South Asian prehistory.

There are so many parallels with the Spanish invasion of the Aztec and Inca civilisations, that it is worth comparison.  In much the same way that the Aztecs, being relatively peaceful, could not contemplate the idea of an invasion as brutal as that of the Spaniards, neither it seems could the Harappans. Here is what happened to the Aztecs:

On the 12th of November, 1519, four days after their entry into Mexico, Cortes and his chief captains went to see the market and the great temple of Tlatelolco with the emperor Motecuhzoma II. They went up the 114 steps of the teocalli and stood on the platform at the top of the pyramid, in front of the sanctuary. Motecuhzoma took Cortes by the hand and told him to look at the great city and all the other towns near by on the lake and the many villages built on the dry land

The Spanish genocide and destruction was almost total.  And those that escaped the genocide later succumbed to disease. 

The Spanish conquest of the Aztec Empire began in February 1519 when Hernán Cortés arrived at the port in Veracruz with about 500 conquistadores, and later moved on to the Aztec capital in his search for gold and other riches.  The ruler of the Aztec empire upon the arrival of the Spaniards was Moctezuma II, who greeted them with civility and showed them the city and who was later killed.  Not only did the Spaniards destroy the city, they brought smallpox with them; Moctezuma’s brother Cuitláhuac was among the first to die from the smallpox epidemic.  Smallpox ravaged Mesoamerica in the 1520s, killing more than 15 million out of a population of less than 30 million.  “Severely weakened, the Aztec empire was easily defeated by Cortés and his forces on his second return.  Smallpox was a devastating and selective disease—it generally killed Aztecs but not Spaniards, who were much more immune to it.”  The Aztecs were defeated because their rules of engagement did not include the wholesale slaughter of its opponent. 

In Harappa, exactly the same thing occurred, the Aryans brought disease with them.   Paleopathological analysis has demonstrated that leprosy and tuberculosis were present at Harappa, with the highest prevalence of both disease and trauma present in the skeletons from Area G (an ossuary located south-east of the city walls). Furthermore, rates of cranio-facial trauma and infection increased through time, demonstrating that the civilization collapsed amid illness and injury.