He was also the local contact for the Sri Lankan government appointed presidential committee to investigate Human Rights violations in the Mannar district.

[3][4][5] On 6 January 1985, Bastian along with 10 others were shot allegedly by the Sri Lankan Army personnel, point blank range in front of the local St. Anne's church.

[3] On January 8, Thomas Savundranayagam, the then Bishop of Mannar, in a statement to the strongly protested the insinuation by the government that arms were found in the church and he also accused the military of complicity in the murder of Father Mary Bastian.

The security forces surrounded the church premises around midnight January 5–6, 1985, entered the back of the mission house, and called Fr Bastian.

After several hours, his body was reportedly removed and put on the steps of a girls school, closed to the convent, photographed after certain objects had been put around it, and in the early hours of January 6 taken away in a white van by uniformed security forces personnel believed to be from nearby Thallady Army camp.The people of Vankalai later erected a statue of Mary Bastian in the compound of St Anne's Church in his memory.