After the formulation of the Aryan invasion theory, archeology did not stop. New finds continued. These however have gradually undermined the invasion theory.

Harappan civilization (3100-1900 BC) was the largest in the world up to its time. Harappan sites have now been found as far west as to the coast of modern Iran, as far north as Turkestan on the Amu Darya river (a region usually identified with the Aryans), as far northeast as the Ganges, and south to the Godavari river. A site has even been found on the coast of Arabia. Thousands of sites have been found with several cities, like Ganweriwala on the Sarasvati river and Dholavira near the ocean in Kutch, as large as the first two major cities found, Harappa and Mohenjodaro. Most sites remain unexcavated and new explorations are likely to push the boundaries of this civilization yet further. A civilization of this size could not have been quickly or easily overrun by either migration or invasion.

Harappan culture maintained a continuity and uniformity that is unparalleled in cultures up to that date. The cities were the best planned of the era, with wide streets and excellent sewage systems. There was a uniformity of arts, crafts, weights and measures throughout the region. Such an organized civilization could not have so easily been taken over, nor could its cultural traditions, particularly its language, be very easily changed, much less eradicated.

It was originally proposed that the Harappan culture was ended abruptly by the Aryan invaders. Evidence however revealed that the sites were abandoned rather than destroyed, along with major ecological changes in the region, with shifting rivers, floods, and desertification of parts of the region, along with the drying up of the Sarasvati river which we have already noted. Unfortunately most historians, particularly from the West, did not know of the importance of the Sarasvati in Vedic literature and merely treated it as a forgotten river to everyone.

Because of this evidence some scholars have given up the idea that the Vedic people destroyed the Harappan culture and proposed that the Vedic people came after the decline of the culture and merely took over the remnants of it. In this it was the abandoned Harappan cities that the Aryans came to, but this view still usually portrayed the advent of the Aryans as violent. This post-Harappan violent invasion I would call "the third birth of the Aryan invasion theory," though it is unclear what they destroyed. It shows the theory already in question.

Other scholars proposed that the Aryans came into the Indus civilization itself during its later period and that Harappan culture was a composite of Aryan and non-Aryan elements, though there is nothing particularly composite about Harappan culture. Most scholars of such views would still like to portray the Aryan advent as violent though no proof for that has ever been found. Meanwhile no evidence of such migrations during the Harappan period has been found either.