Akbar's alliance with the Rajputs had created the Mughal Empire and the end of that alliance by Aurangzeb prepared the ground for the destruction of that empire. This alliance was in large measure the product of Akbar's personality---the ability to rise above religious predilection and tribal instincts to attract capable men from different communities to one's side. His successors Jehangir and Shah Jahan were however bigoted and their intolerance showed up in several instances, but considering the undeniable importance of the large Hindu population and the collective military power of the Rajput clans, they curbed their hatred in the interests of the empire. In this spirit, Shah Jahan warned the youthful Aurangzeb against being unfriendly towards the Rajputs---however the warning seems to have been shrugged off.
In 1679 Maharaja Jaswant Singh Rathor was dead and Aurangzeb had occupied his Kingdom of Jodhpur and its many forts and towns. The Rathor clan allied with the Sesodias of neighboring Udaipur and thus began what is called "the Rajput war". The full force of the Mughal Empire, commanded by Aurangzeb in person, descended on Rajputana but the two Rajput clans, instead of defending every little district or fort, withdrew into the craggy hills and forested valleys of the Aravalli Range. From this base they fought off the invaders and launched counter-attacks of their own---so successful was this strategy that Aurangzeb's sons and generals refused to take offensive actions and despaired of victory.
Things came to such a pass that the Emperor's favorite son Akbar joined a conspiracy with the Rajput clans to overthrow his father and restore the old policies of the empire.
Illustrated in the Adab-i-Alamgiri---Aurangzeb's letters to his father where he tried to pacify Shah Jahan by promoting a Rajput chieftain, Rao Karan of Bikaner, to a higher post. On becoming Emperor he was forced to tolerate the established Rajput generals of his father's time and continued to use them in campaigns.
Sir Jadunath Sarkar calls Jodhpur the largest Hindu state in North India whose leader could organize opposition to Aurangzeb's policy of Islamization.
The attempt failed but the Rajputs had effectively turned the tables on Aurangzeb by hailing his son as Emperor Akbar II. Since the new Emperor could not be safe within his father's reach the Rajputs escorted him through the intervening Mughal provinces to the safety of the Maratha Kingdom. Shambhuji welcomed the royal guest and promised to aid him in marching north, uniting with the Rathors and Sesodias (the two greatest Rajput clans), and taking possession of the Mughal throne. This event and the projected plans of these two personalities changed the history of India.
Aurangzeb had to leave the task of Islamizing North India unfinished and was forced to rush all his forces south into the Deccan. He blockaded the Maratha Kingdom from the land and assisted the sea-based powers in their war against Shambhuji. For five years (1681-86) this strategic disposition continued and it was only in 1686 that Akbar II struck northwards. But his attempt, of joining the Rajputs and then marching on to Delhi, was foiled---at the end of that year the disappointed youth left for Persia. His last attempt had been prompted by Aurangzeb's increasing troubles with new enemies.
While prosecuting his war against the Maratha Kingdom Aurangzeb had sent diplomatic appeals to both Bijapur and Golconda to assist him in that war, or at least to stand aside. The Sultanates made no response to the appeals and instead gave secret help to the Marathas---a look at the map makes the reason amply clear. As long as the Maratha Kingdom existed on the flank of the Mughal territory, the Mughal governor of the Deccan could not march against Bijapur or Golconda in strength (see experience of Dilir Khan against the Berads of Sagar). Shivaji and Shambhuji were the only guarantees for the continued survival of these worthless states. At last in 1685 Aurangzeb decided to increase the pressure on Shambhuji by annexing Bijapur---after a long siege he became the master of the devastated city. Towards the end of 1687 Aurangzeb marched into the similarly ruined and heavily bombarded capital of Golkonda:
Akbar continued to style himself Emperor in all official communications until his departure from India.
These were the Portuguese and the Siddis; their contest with the Marathas had begun early in the time of Shivaji and related to the safety of Maratha shipping and Maratha subjects living along the coast.
Akbar II had many supporters even as late as in 1685; in the words of the English factors at Surat, "We have frequent alarms here of all the Rajputs being in arms to assist Sultan Akbar backed by many of the Muslim nobles dissatisfied to the Emperor." Sardar Tarin an Afghan in the Emperor's camp used to recruit soldiers and send them to serve Akbar; Abdus Shakur and his 180 Uzbek soldiers joined the rebel Prince; in 1685 4000 rebels at Broach proclaimed Akbar as their true Emperor. Half-hearted attempts were also made to unite father and son but Akbar's harsh sentence of deposition of his father, publicly announced, had created immense hatred between the two.
The Sultanates were at the last stage of their existence; their territories were divided between rival generals and tributary indigenous rulers were practically independent.
In these two years Shambhuji was faced with numerous rebellions and conspiracies within his Kingdom even as he sent forces to assist the Sultanates or made diversionary attacks on Mughal territory. But the rebellions took the wind out of these brave attempts and Shambhuji sought relief by turning to drink and revelry. In such a state he was finally captured by the Mughals in January 1689 and executed. A great pall of terror had lifted from the heads of the Mughal soldiers and nobles who now energetically besieged Maratha forts and by the end of 1689 captured most members of the Maratha royal family---all except Shambhuji's step-brother, and hastily crowned King, Rajaram.
By 1690 Aurangzeb was the unrivalled master of the Deccan---Rajaram had fled far in the south to Shivaji's possessions in the Carnatic. Before leaving, he appointed Ramchandra Bavdekar the supreme commander of the war in the Maratha homeland with lieutenants like Parashuram Trimbak and Shankarji Narayan. Safe in the southern fort of Jinjee Rajaram appointed Prahlad Niraji his supreme regent to be assisted by generals like Dhana Singh Jadav and Santa Ghorpade. Thus the Marathas calculated that Aurangzeb would be forced to divide his forces into two, separated by several hundred kilometers, and this would save the Maratha homeland from complete conquest.
Within fifteen years Aurangzeb was on the retreat and the Deccan, economically ruined and depopulated by war and pestilence, lay prostrate under the Marathas. How did this sudden change from near dominance to total defeat happen? A contemporary writer, traveling with Aurangzeb's army, tried to answer this question in the following words: "Rajaram, who succeeded Shambhuji, lost his capital and had to flee to Jinjee. So the Maratha state servants supported themselves by plundering on all sides, and paying a small part of their booty to the King...In despair of getting their monthly salaries regularly, they regarded the plunder of Mughal territory as a gain and a means of maintaining themselves."
But on the other side was Mughal success in conquering southern India. Decades after Aurangzeb's death the biggest Muslim kingdoms were established in the south: Hyderabad, Carnatic, and Mysore. But this spread of the Mughal empire contained within itself the seeds of its break-up for these reasons:
Mughal weakness: the conquest of Bijapur and Golconda brought no gain to Aurangzeb. These Shia Sultanates were at the last stage of their existence; their individual ministers and tributary chiefs were more powerful than the governments at each capital. The Mughal annexation of Muslim Kingdoms in North India had been a smooth process, by which the nobles of those states were enrolled into the Mughal military system and the wealth of the annexed state paid for the expenses of its conquest. Neither of these things happened in the south---the Mughals had to take out military expeditions into the estates of the Bijapuri and Golkonda nobles before they submitted. Even then these nobles and indigenous chiefs sighed for their former independence and found ready support from the numerous Maratha armies in the field, further complicating the military situation for the Mughals.
Mughal Finances: For the reasons cited above, and also due to the Maratha plunder, the Mughal army could not live off the conquered land and had to be sustained on the revenues from the Northern provinces. Thanks to Aurangzeb's bigotry even the north was restless and burning with strife and eventually the treasure of three generations, stored at Delhi and Agra, had to be opened and sent to Aurangzeb. This movement of money and material to the south was an easy target for the Maratha armies, who found a wonderful source of wealth to sustain them for a long time. It was remarked by a contemporary writer, "I have heard that every week the Marathas give away sweets and money in charity, praying for the long life of the Emperor who had proved to be the feeder of the universe for them!"
Mughal administration: In the Mughal army the nobles were assigned estates where they could retire after campaigning. But the estates in the Deccan and the Carnatic suffered from Maratha plundering; the local villagers joined the raiders rather than engaging in the thankless task of farming while paying rent and revenue to two sets of masters! This quote from a contemporary historian illustrates this system, "The powerful headmen of certain villages, in concert with the Marathas, built small forts and refused to pay revenue." Several Marathas also collaborated with Mughal generals while looting the common people. The foreign breeds of horses, so important for the Mughals, did not last long in the heat and humidity anyway but their non-stop use in campaigning without any rest or repose wore them out even further.
Aurangzeb's letter to his general Nusrat Jang, from the Ruka'at-e-Alamgiri, reads, "My sincere Nusrat Jang, our whole energy was devoted to the conquest of the Deccan. Thank God that we have accomplished that work. But the expenses incurred are defrayed from the treasury of Northern India. We are still in debt."
This Deccani system of war, where light cavalry hovered around each Mughal army, plundered and reduced the country around to dust and then swooped down in lightning charges when the enemy's guard was lowered, was termed ghanimi qawait in the Persian histories. Ghanimi translated to "light forays" qawait to "tactics". The Central Asian soldiers in the Mughal army instantly recognized this method of warfare as similar to what their kinsmen practiced in that steppe land---particularly the Kazzaks. Hence another word for this system of war was Kazzaki.
And this light cavalry had no base, no stronghold, whose blockade or destruction would destroy its power. The women and children of the Marathas were of course lodged in the forts of their homeland; but whenever the Mughals besieged these strongholds the Marathas would pull out their families and take them away to the forts of the Berads or of the Portuguese or even far south to the relative safety of the southern region. Having done that these Marathas would then hover around the besieging army, cut-off its supply lines and swoop down on isolated groups of soldiers and camp followers. Such was their impact that the Mughals had to build mud walls around their camps and siege lines to protect their men from the Maratha light cavalry---the besiegers effectively became the besieged!
Even with these factors it should not be assumed that the Marathas had it easy against their enemies---their superiority became apparent only towards the close of the 17th Century. Up to that time there were continuous diplomatic negotiations between the leaders of the two sides and several Maratha chiefs sought legitimacy and rank from the Mughal Emperor and served him loyally against their own brethren. This wasn't unusual---in the same manner Sikh chieftains accepted Ahmad Shah Abdali's rule and alliance with his generals even after the Afghans had committed great outrages on the Sikhs and their religion. Similarly Rajput chieftains sought service under Aurangzeb even after their faith had been attacked and their people subjected to jaziya. In the end wars are about politics and money as much as they are about religion or ideology.
Such was the origin of the "Maratha wall" around European factories and its variant, the "Maratha ditch", dug out to break the advance of light cavalry.
Some of these had been dispossessed by Shivaji, some had rebelled against Shambhuji, and some sought financial gain by allying with the Mughals. Those that remained loyal to the Mughal cause were the Jadavs of Sindhkhed (Shivaji's mother's family), Kanhoji Shirke and his sons (Rajaram's mother's family), Nagoji Mane, the Dafles of Jath, and several thousand Mavle infantry under individual Mughal or Maratha commanders.
Shias too had mourned the loss of the Shia Sultanates of Bijapur and Golconda and there were several instances of Mughal oppression against the Shias but chiefs of that sect continued to serve the Mughal Empire for money and position.