Chota Rajan is believed to have assisted intelligence agencies in getting a low down on the activities of the D Company and its members using his intimate knowledge of the gang and its operations. To demonstrate his claims of being a Hindu don, Rajan threatened to kill those accused of engineering the Bombay bomb blasts. The most prominent accused to be killed was Saleem Kurla in April 1998, followed by Mohammad Jindran in June 1998 and Majid Khan on March 1, 1999. The D Company retaliated by killing Shiv Sena pramukh Mohammad Saleem. The Shiv Sena, which ruled Maharashtra along with the BJP from 1994 to 1999, is believed to have a soft corner for the ‘Hindu Don’. It is alleged that selective police action against the Dawood gangsters during the Shiv Sena regime and their elimination in encounters helped strengthen Rajan’s position, just as Dawood himself had benefitted in the 1980s. The Sena laid bare its affection for Chota Rajan in an editorial in Saamna, its mouthpiece, edited by Bal Thackeray. The editorial heaved a sigh of relief, attributing Chota rajan’s survival to “good fortune’." Saamna alleges that Pakistani ISI was behind the move to kill Chota Rajan.
In February 2010, Chotta Rajan gang assassinated Jamim Shah, a third-generation Nepali media baron of Muslim Kashmiri origin. Shah allegedly had links with Dawood Ibrahim and Pakistan's Inter Services Intelligence (ISI) and was the kingpin of a racket producing fake Indian money in the Himalayan nation. His anti-Indian activities had rankled New Delhi for more than a decade and half.