Well, the proximate cause for the breakup of the Mughal Empire were the Marathas. The final 30 years of Aurangzeb’s rule were a more-or-less continuous campaign against the Marathas, which bankrupted the Mughal treasury. It consisted of numerous battles and skirmishes, none of which were decisive in the long run. Territories kept changing hands repeatedly as Aurangzeb would send the huge Mughal army to capture a given town or fort, but the Marathas would take it back, and it would have to be recaptured over and over. Towards the end, it became increasingly hard for the Mughal army to hold Maratha land, and after Aurangzeb died, the Marathas launched their own attack on the Mughal Empire, breaking it up and replacing it with the Maratha Empire.
The biggest pieces that remained were Hyderabad in the far south, Bengal in the east, and Oudh in the area of UP. They became independent kingdoms, ruled by Nawabs. The Maratha Empire took over most of the territory owned by the Mughals, bounded by Bengal in the east, Hyderabad in the south, and the Durranis of Afghanistan in the west. The Mughal “Emperor” formally remained, but his rule was confined to Delhi and its immediate environs, and Mughal Emperors were basically Maratha-appointed puppets. This continued until the Martha Empire itself split up, and its pieces were taken over by the British, after which the Mughal Emperors remained as British puppets. There was a brief resurgence in 1857 during the Mutiny, when the mutineers declared Bahadur Shah Zafar “Emperor of India”. But it was quickly defeated by the British and the Emperor sent off to exile in Burma, where he died. He was the last Mughal Emperor.
In the broader context, Mughal rulers had been mostly fair and mild since the time of Akbar, who was among the first of the Mughals who viewed himself as Indian rather than as a foreign invader just there for the loot. He enacted a bunch of laws that treated Indians more-or-less equitably, and for the most part, did not offend the Hindu majority. His successors Jahangir and Shah Jahan did not deviate much from his policies, though they were poor administrators compared to Akbar.
But his great grandson Aurangzeb was something of a hardline Islamist. Aurangzeb established a council to create a set of laws fully compliant with Islam – the Fatawa-e-Alamgiri, which despite the name isn’t really a fatawa but rather a fiqh type 30-volume compendium of Islamic law. Among his council were a hundred Islamic scholars from Saudi Arabia, the same guys who later produced Wahabbism. It was a very strict version of Hanafi Islam, quite intolerant towards the Hindu majority, imposing numerous taxes and humiliations.
This led to a series of revolts that plagued the latter half of Aurangzeb’s long reign. They include the Jatt rebellion of Mathura/Bharatpur, the Rajput rebellion in Marwar, the Ahom rebellion in the east, the Satnamis in Haryana, etc. Many of these were never settled, for example, with Aurangzeb fighting the Rajputs until he died, when they immediately broke away. Others were technically “put down” by the Mughal army, for example the Jatts were defeated when they established the State of Bharatpur, but the resentments never died, and Aurangzeb would periodically have to return to deal with fighting that would break out again and again.
But the biggest problem he had to deal with was the Maratha wars, which began when he invaded Bijapur in 1680. From that point on until Aurangzeb died in 1707, he was involved in a long series of wars that continually interrupted his campaigns down south, and his frequent returns to the north to put down one rebellion or the other. The Marathas were guerilla fighters, not directly taking on the huge Mughal army that greatly outnumbered them, but experts at splitting it up by attacking simultaneously at different places, then focusing on one piece at a time. When the Mughals attacked their forts, the Marathas would often withdraw their main forces, leaving the fort defended by a small suicide contingent of troops whose job was to inflict as many casualties as they could before they died. Then when the Mughals took the fort and moved on, the main army would return to reclaim the fort. Some forts changed hands as many as a dozen times during the wars.
By the time Aurangzeb died in 1707, large parts of his empire were in rebellion. The Marathas weren’t done with the Mughals either, they pushed into Mughal lands and took over most of the Mughal Empire. By around 1750, they controlled the bulk of what is now India, bounded by Bengal in the east (under the Nawabs of Bengal, soon to be displaced by the East India Company after the Battle of Plassey in 1757), the Nizam of Hyderabad in the far south and the Durranis in the west. Delhi remained under Mughal rule, and part of UP under the Nawab of Oudh.
There was a long series of short-lived Mughal “Emperors” in this period, who ruled nothing except a bit of land around Delhi, but they were the claimants to the Mughal throne, and so still maintained some legitimacy. The Marathas saw an advantage in maintaining this tradition, and some of the later Mughal Emperors such as Shah Alam were basically puppets under Maratha control.
This remained the status quo until the Marathas split up and were eventually defeated by the British, after which the Mughal Emperors became British puppets instead of Maratha puppets. After the last Mughal Emperor was exiled by the British, the Mughal dynasty finally came to an end.
The premise of your question is incorrect. The Mughal empire covered most of India in 1707. However, after Aurangzeb's death in 1707(the last of the 'great' mughal emperors) it fell rapidly. Aurangzeb ruled for 49 years until 1707. From 1707 until 1759 there were a total of 11 emperors! including 7 from just 1707 to 1719. Muhammad Shah's reign (1719-48) saw the sack of Delhi by the Persian invader Nadir Shah in 1739. This was a final nail in the coffin for the legitimacy of the Mughals. It was a period of chaos and the empire disintegrated pretty rapidly. The Marathas were the largest of the hindu kingdoms that gained territory during this period. When the British started taking over India starting 1757, the largest Indian empire was actually Maratha not Mughal. The Mughals were reduced to titular roles with actual influence in and around Delhi. So it would be accurate to say that the Marathas took over from the Mughals and the British took over from the Marathas.
Maratha empire (in yellow) during 1760 (greatest extent) https://en.wikipedia.org/wiki/Maratha_Empire#/media/File:India1760_1905.jpg
Mughal Empire Maximum extent in 1707 (greatest extent) http://media-2.web.britannica.com/eb-media/07/1607-004-B9810CCD.jpg