Elephant Pass has been home to a strategic military base since 1760, when the Portuguese built a fort there, which was later rebuilt and garrisoned by the Dutch in 1776[5] and later by the British.

By this time the Sri Lanka Army base at Elephant Pass had been expanded with a complex of military installations under the command of the 54 Division with over 5000 personnel attached.

Given these circumstances, LTTE leader Prabakaran changed his strategy to take Elephant Pass by gradually encircling and weakening the troops inside, cutting off supplies and, in effect, strangling the base.

LTTE planned Operation Unceasing Waves III with the objective of taking control of the peninsula and launched its first stage on 11 December 1999 with seaward landings at Vettalankerny east of Elephant Pass, engaging the 2nd Gemunu Watch which had been deployed there.

On 17 December the Sri Lanka Air Force lost a Mil Mi-24 while repulsing a seaward attack by the LTTE on Thamilamadam, its pilot Squadron Leader Tyron Silvapulle was posthumously awarded the Parama Weera Vibhushanaya.

Reinforced by the 3rd Sri Lanka Light Infantry, this line held, and the LTTE began infiltrating it with cadres dressed in army uniform.

Maj. Gen. Sarath Munasinghe, who had been the Commander, SFHQ-J from 11 November 1999 to 12 December 1999, had retired and been succeeded by Maj. Gen. Nihal Jayakody, who died on 19 January 2000 after having suffered a heart attack.

Maj. Gen. Egodawela crossed over in a tank and his deputy Brigadier Percy Fernando remained behind to move with the troops, commanding the rear guard for a fighting withdrawal.

Over 300 troops were killed and 500 wounded in the withdrawal, including the senior officers of the 54 Division—Brigadier Percy Fernando, Col. Bhathiya Jayatilleka, Col. Rohitha Neil Akmeemana, Col. Harish Hewarachchi and Lt. Col. Hewage Hewawasam.

[6][8][9] Fighting continued until mid-May for control of the Jaffna peninsula, and by 9 May Deputy Defence Minister Anuruddha Ratwatte reported that 758 soldiers had been killed, 2,368 had been wounded and 349 were missing since the battle for Elephant Pass started on 22 April.

[11][12] Barely days before the fall of the Elephant Pass base, President Chandrika Kumaratunga made some abrupt changes in the defense structure; retired Chief of the Defence Staff Rohan Daluwatte was placed in overall charge of the three services, Gen. Janaka Perera was made Northern Province Commander and Gen. Sarath Fonseka the Jaffna Commander; the former had insisted on the latter.

[6][14] Despite gaining footholds in the areas of Chavekachechri and Ariyalai, the LTTE was forced to retreat to the Muhamalai and Nagarkovil defensive lines after suffering heavy losses from artillery and airstrikes.

[15][16] Although the fall of Elephant Pass was seen as a great triumph, a series of setbacks highlighted LTTE's weakness against conventional military forces in regular conflict.

On 3 September 2000 the army mounted a massive counteroffensive, named "Agni Keila", to retake some of the LTTE-held territories to the south of its defensive lines, but after advancing a few kilometers the troops met heavy resistance.

Sri Lankan troops and Tamil Tiger rebels fought pitched battles for control of the peninsula, which left hundreds dead in a matter of months.