During the 1971 War, Mulla was commanding the 14th anti-submarine squadron, a task force that formed part of the Western Fleet. The squadron consisted of the INS Khukri (F149), INS Kirpan (F144) and INS Kuthar (F146).[7] The squadron was assigned the task of hunting and destroying enemy submarines in the North Arabian Sea. At 2050 hours on 9 December 1971, his vessel, INS Khukri, was hit by a torpedo fired by an enemy submarine, PNS Hangor, about 64 kilometres (40 mi) off Diu. He issued orders for the ship to be abandoned because it was sinking.[8] He chose to go down with the ship in the highest traditions of the Indian Navy. Mulla was decorated with the Maha Vir Chakra, the second-highest gallantry award.
Two ships of the Indian Navy under the command of Captain Mahendra Nath Mulla, Senior Officer of a Frigate Squadron were assigned the task of locating and destroying a Pakistan Submarine in the North Arabian Sea. During these operations on the night of 9 December 1971, in ship KHUKRI was hit by torpedoes fired by an enemy submarine and sank. Having decided to abandon the ship, Captain Mulla without regard for his safety supervised the arrangements for the rescue of his ship’s company in a very cool, calm, and methodical manner. Even at a later stage whilst the ship was sinking, Captain Mulla showed presence of mind and continued to direct rescue operations and refused to save himself by giving his own life saving gear to a sailor. Having directed as many of his men as possible to leave the ship, Captain Mulla went back to the bridge to see what further rescue operations could he performed. In doing so, Captain Mulla was last seen going down with his ship. His action and behaviour and the example he set, has been in keeping with the highest traditions of the service. Captain Mahendra Nath Mulla has displayed conspicuous gallantry and dedication.