The affection amongst India and the Tamil Tigers did not last long following the suspicion of the Tamil Tiger camp that India was actually helping Tamil rebels for having their own secret agenda. In 1986 Tamil Tigers also decided to separate themselves from ENLF & began to engage in armed contact with other Tamil rebel groups. The conflict between the rebels was won by the Tamil Tigers & members of the defeated Tamil rebel group joined into the Tamil Tigers.
In 1987, relations between India & Sri Lanka about the conflict in Tamil entered a new phase after negotiations between the two resulted in an Indo-Sri Lanka Accord. Under the deal, Sri Lanka pledged to grant special autonomy to the Tamil regions & instead, India will send its troops to aid the demilitarisation process. At the point when the Tamil Tigers refused to stop its armed activity, the conflict between Indian troops and Tamil Tigers broke out, finally in 1990, Indian troops withdrew from Sri Lanka with the loss of 1,200 personnel and financial loss 10.3 billion rupees.
Ahead of India’s Sri Lanka retreat, in 1989 the Tamil Tigers and the government agreed to a ceasefire in the same year. However, the phase of the ceasefire did not last long after in June 1990, Tamil Tigers personnel fired on & killed 600 unarmed police in East Sri Lanka police stations. A few months later alias in August 1990, the Tamil Tigers attacked 4 mosques & killed 147 local Muslims inside. As a result of the attack, the Sri Lankan Muslim community, initially neutral during the conflict, turned against the Tigers and supported government troops.
Following the end of the cease-fire phase, the armed conflict between Tamil & Sri Lankan Tigers broke out again where the intensity of the conflict grew. The climax was that in 1991, about 5,000 Tamil Tigers soldiers surrounded the military headquarters of the Elephant Pass located near the Jaffna Peninsula. The fighting was furious, but Sri Lankan troops could finally defend the military headquarters after they received an extra 10,000 troops join to the battle. As a result of the battle, each party reportedly lost 2,000 personnel.
During the decade of the 1990s, conditions on the battlefield coloured the tug of war between the Sri Lankan government troops & Tamil Tigers troops in which the Tamil Tigers initially successfully cornered the troops of Sri Lankan government in the north before then troops Tamil Tigers successfully beaten back in 2000. In this period also, suicide bombings carried out by Tamil Tigers throughout Sri Lanka are also becoming more frequent. The most phenomenal example of a suicide bomb attack in this period was the May 1993 attack that killed the then Sri Lankan President Ranasinghe Premadasa.