Yogeswaran was apparently briefed to patch up the relationship with the LTTE and Amirthalingham. It was later reported that Yogeswaran had held four meetings with two LTTE men to forge unity among the different Tamil militant groups and also with the TULF.

Subsequently, he arranged a meeting between the LTTE and Amirthalingham, at 7pm on July 13, 1989. That evening Amirthalingham and Sisvasithamparam were due to attend a dinner party hosted by the Indian High Commissioner in Colombo, at the Hotel Taj Samudra, in honor of B G Deshmukh, the Principal Secretary, who had delivered the last letter from Rajiv Gandhi to the Sri Lankan president.

Yogeswaran told the sub-inspector of police, Thambirajah Kandasamy, about the visitors and requested him not to search the visitors. But, Kandasamy protested and told Yogeswaran, `We cannot trust these fellows, sir.` Yogeswaran replied, `They are our guests. They will feel insulted and would stop coming to meet us.` So, Kandasamy, though not satisfied with Yogeswaran`s explanation, agreed to his request.

At 6:45pm on July 13, three LTTE men, who were later identified as Visu, alias Rasiah Aravindarajah, one-time Vavuniya leader of the political wing of the LTTE, his assistant Peter Aloysius Leon and Vignan arrived at the residence. Sathiyamoorthy, the guard at the gate, demanded identification and they told him that they were from the LTTE and handed over their national identity cards. At this stage, Kandasamy appeared at a first-floor balcony and told the guard to allow the visitors in without a body-search. This was a tragic security lapse. Visu and Aloysius went upstairs to Yogeswaran`s apartment, while the third man stayed at the gate.

Later the visitors and the TULF leaders sat down and began their conversation. Everyone laughed and was relaxed. Amirthalingham explained to the LTTE youths that lack of unity was hurting the Tamil cause and the internecine fighting was eroding world sympathy. Conflict among the Tamils group was giving the government an opportunity to delay the devolution process. He assured Visu that the LTTE would be accorded a pre-eminent position in any united arrangement and told him to convey his sentiments to the LTTE leadership and persuade them to come to an arrangement with other Tamil groups.

Yogeswaran`s wife served refreshments to the men. Once Visu and Aloysius finished their drinks, they rose to place their tumblers on the table, then they turned together and pulled out their revolvers, firing at the TULF leaders. Amirthalingham was hit in the head and Yogeswaran on the chest and stomach, and Sivasithamparam on his right shoulder. The gun shots aroused the security chief Kandasamy, who rushed to find Visu and Aloysius still firing. He opened fire with his service revolver and the LTTE assailants backed off. Another guard fired from the balcony at the fleeing men and both assailants were shot. Meanwhile, in the commotion, the guard at the gate shot and killed Vignan, the third member of the assassination squad. Yogeswaran and Amirthalingham died from the gunshots, while Sivasithamparam escaped with injuries to his collarbone and was able to give a detailed statement from his hospital bed.
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Meanwhile, as usual, the LTTE denied involvement in the killings and blamed `diabolical forces at work to disrupt the on-going peace talks between the LTTE and the Sri Lankan government`. It was interesting to note that Adele Balasingham, who was at that time staying with the LTTE delegation in Colombo, purposely avoided mentioning even one sentence about the assassination of Amirthalingham in her book The Will to Freedom. She might have to explain one of these days the reason for omitting the recording of the deaths of a Tamil leader whose career spanned the political horizon of Sri Lanka for well over four decades.