During the 1990s, however, escalating tensions and conflict due to separatist activities in Kashmir, some of which were supported by Pakistan, as well as the conducting of nuclear tests by both countries in 1998, led to an increasingly belligerent atmosphere. In an attempt to defuse the situation, both countries signed the Lahore Declaration in February 1999, promising to provide a peaceful and bilateral solution to the Kashmir conflict.During the winter of 1998 -1999, some elements of the Military of Pakistan were covertly training and sending Pakistani troops and paramilitary forces, some allegedly in the guise of mujahideen, into territory on the Indian side of the LOC. The infiltration was code named "Operation Badr"; its aim was to sever the link between Kashmir and Ladakh, and cause Indian forces to withdraw from the Siachen Glacier, thus forcing India to negotiate a settlement of the broader Kashmir dispute. Pakistan also believed that any tension in the region would internationalise the Kashmir issue, helping it to secure a speedy resolution.
Some analysts believe that the blueprint of attack was reactivated soon after Pervez Musharraf was appointed chief of army staff in October 1998. After the war, Nawaz Sharif, Prime Minister of Pakistan during the Kargil conflict, claimed that he was unaware of the plans, and that he first learned about the situation when he received an urgent phone call from Atal Bihari Vajpayee, his counterpart in India. Sharif attributed the plan to Musharraf and "just two or three of his cronies", a view shared by some Pakistani writers who have stated that only four generals, including Musharraf, knew of the plan. Musharraf, however, asserted that Sharif had been briefed on the Kargil operation 15 days ahead of Vajpayee's journey to Lahore on February 20.
During the winter season, due to extreme cold in the snow-capped mountainous areas of Kashmir, it was a common practice for both the Indian and Pakistan Armies to abandon some forward posts on their respective sides of the LOC and to reduce patrolling of areas that may be avenues of infiltration. When weather conditions became less severe, forward posts would be reoccupied and patrolling resumed.During February 1999, the Pakistan Army began to re-occupy the posts it had abandoned on its side of the LOC in the Kargil region, but also sent forces to occupy some posts on the Indian side of the LOC. Troops from the elite Special Services Group as well as four to seven battalions of the Northern Light Infantry (a paramilitary regiment not part of the regular Pakistani army at that time) covertly and overtly set up bases on the vantage points of the Indian-controlled region. According to some reports, these Pakistani forces were backed by Kashmiri guerrillas and Afghan mercenaries.
Pakistan's military aim for carrying out the intrusions was based on exploitation of the large gaps that exist in the defences in the sector both on Indian and Pak side of the Line of Control (LoC). The terrain is extremely rugged with very few tracks leading from the main roads towards the LoC. During winters the area gets very heavy snowfall making movement almost impossible. The only mountain pass connecting the Kargil area to the Kashmir Valley, Zoji La, normally opens by the end of May or beginning of June. Thus, moving of reinforcements by surface means from Srinagar would not have been possible till then. Pakistan Army calculated that even if the intrusions were discovered in early May, as they were, the Indian Army's reaction would be slow and limited, thereby allowing him to consolidate the intrusions more effectively. In the event, however, Zoji La was opened for the induction of troops in early May itself. The intrusions, if effective, would enable Pakistani troops to secure a number of dominating heights from where the Srinagar-Leh National Highway 1A could be interdicted at a number of places. The intrusions would also draw in and tie down Indian Army reserves. The intrusions would, further, give Pakistan control over substantial tracts of strategic land area across the LoC, thereby, enabling Islamabad to negotiate from a position of strength. The intrusions would irrevocably alter the status of the LoC.
Apart from keeping the plan top secret, the Pakistan Army also undertook certain steps to maintain an element of surprise and maximise deception. There was no induction of any new units or any fresh troops into the FCNA for the proposed operation. Any large-scale troop movement involving even two or three battalions would have drawn the attention of the Indian Army. The Pakistan Army artillery units, which were inducted into the FCNA during the heavy exchange of fire from July to September 1998, were not de-inducted. Since the exchange of artillery fire continued thereafter, though at a lower scale, this was not considered extraordinary. There was no movement of reserve formations or units into FCNA until after the execution of the plan and operations had begun with the Indian Army's response. No new administrative bases for the intrusions were to be created, instead they were to be catered for from those already in the existing defences. The logistic lines of communication were to be along the ridgelines and the nullahs well away from the tracks and positions of the Indian Army troops already in position. After it was finalised, the plan was put into action towards the end of April. The main groups were broken into a number of smaller sub groups of 30 to 40 each for carrying out multiple intrusions along the ridgelines and occupy dominating heights.
Initially, with little knowledge of the nature or extent of the infiltration, the Indian troops in the area assumed that the infiltrators were jihadis and claimed that they would evict them within a few days. Subsequent discovery of infiltration elsewhere along the LOC, and the difference in tactics employed by the infiltrators, caused the Indian army to realize that the plan of attack was on a much bigger scale. The total area seized by the ingress is generally accepted to between 130 km² - 200 km²; Musharraf, however, stated that 500 square miles (1,300 km²) of Indian territory was occupied.
The Government of India responded with Operation Vijay, a mobilisation of 200,000 Indian troops. However, because of the nature of the terrain, division and corps operations could not be mounted; subsequent fighting was conducted mostly at the regimental or battalion level. In effect, two divisions of the Indian Army, numbering 20,000, plus several thousand from the Paramilitary forces of India and the air force were deployed in the conflict zone. The total number of Indian soldiers that were involved in the military operation on the Kargil-Drass sector was thus close to 30,000. The number of infiltrators, including those providing logistical backup, has been put at approximately 5,000 at the height of the conflict. This figure includes troops from Pakistan-administered Kashmir who provided additional artillery support.The Indian Air Force launched Operation Safed Sagar in support of the mobilization of Indian land forces, but its effectiveness during the war was limited by the high altitude and weather conditions, which in turn limited bomb loads and the number of airstrips that could be used.The Indian Navy also readied itself for an attempted blockade of Pakistani ports (primarily Karachi port) to cut off supply routes. Later, the then-Prime Minister of Pakistan Nawaz Sharif disclosed that Pakistan was left with just six days of fuel to sustain itself if a full-fledged war had broken out. Once again the Indian armed forces showed considerable resilience and innovation. Traditional artillery pieces were changed from their usual role of lobbing shells over mountains to a direct fire mode - targeting line-of sight Pakistani bunkers and supply dumps. In an act that was probably not anticipated by Pakistan - the Indian Air Force was brought in, and once again innovation was applied to achieve pinpoint accuracy in high altitude bombardment of mountaintop targets in conditions that no other air force in the world has been asked to perform. Though Indian forces initially suffered some losses, they were able to gain control of various heights very quickly. From Patalik to Chorbatla, from Valdor to Shangruti, the Indian soldiers were victorious everywhere. The Pakistanis were surrounded from all sides. Despite fighting uphill, the brave Indian officers and jawans cut through the Pakistani barricades. And for once the nation stood united like never before. The religion was relegated to the background and all communities were one. From Kashmir to Kanyakumari there was an outpour of emotion for the valiant Indian soldiers. Every time a body returned from the battlefield, entire nation shed tears and only vowed with further resolve to show no mercy for the Pakistanis. A newly empowered media savvy Indian public and the media aided mobilization of resources and watched India's first televised war as territory was recaptured peak by peak. A beleagured Pakistani Prime minister, Nawaz Sharif, expecting his country to be invaded (mistakenly as it turned out) rushed to the US to try and work out a belated admission of Pakistani involvement and a withdrawal. By the time he returned to face an angry population the rout was complete, and the territorial advantage that Pakistan had painstakingly built up through years of benign Indian neglect was wiped out.
Following the outbreak of armed fighting, Pakistan sought American help in de-escalating the conflict. Aide to then President Clinton reported that the US intelligence had imaged Pakistani movements of nuclear weapons to forward deployments for fear of the Kargil hostilities escalating into a wider conflict between the two countries. However, President Clinton refused to intervene until Pakistan had removed all forces from the Indian side of the Line of Control. Following the Washington accord on July 4, where Sharif agreed to withdraw Pakistani troops, most of the fighting came to a gradual halt, but some Pakistani forces remained in positions on the Indian side of the LOC. In addition, the United Jihad Council (an umbrella for all extremist groups) rejected Pakistan's plan for a climb-down, instead deciding to fight on. The Indian army launched its final attacks in the last week of July; as soon as the Drass subsector had been cleared of Pakistani forces, the fighting ceased on July 26. The day has since been marked as Kargil Vijay Diwas (Kargil Victory Day) in India. By the end of the war, India had resumed control of all territory south and east of the Line of Control, as was established in July 1972 as per the Shimla Accord.