[2] Unlike his predecessor, Loya allowed Amit Shah, the national leader of the Bharatiya Janata Party (BJP) who had been accused of ordering the murder of Sohrabuddin Sheikh, to be exempt from appearing at the court in person, until the framing of charges,[2] except when Shah was already in the state of Maharashtra, where the case was being litigated.
[6] On 30 December 2014, Loya's successor in the special CBI court, M. B. Gosavi, dismissed all charges against Shah in the Sohrabuddin Sheikh case, and ruled that he need not stand trial.
Kapil Sibal of the Congress claimed that Khandalkar was thrown of a roof building in November 2015, while Thombre died “suspiciously while traveling in train from Nagpur to Bangalore on May 16, 2016, in Hyderabad” [11][12] The Congress asked for an investigation by an independent SIT monitored by the Supreme Court of India, claiming that even the post mortem report was manipulated.
[13] On 12 January 2018, Justices Jasti Chelameswar, Ranjan Gogoi, Madan B. Lokur and Kurian Joseph, the second- to fifth-most senior judges of the Supreme Court, held a press conference, in which they warned that the integrity of the court was under threat, and accused Dipak Misra of allocating cases selectively, based on personal preference.
Dushyant Dave, arguing for an independent probe into Loya's death, asked "Why would a chief justice of the high court call the boy and issue a statement, just days before retirement?
You should have killed me with a bullet rather than attacking my reputation.”[23] Later, he recused from the case and requested the Chief Justice of India, Dipak Misra, to constitute another bench.
[24] Later, Dr RK Sharma, the former head of the Forensic Medicine and Toxicology Department at the All India Institutes of Medical Sciences in Delhi, and the president of the Indian Association of Medico-Legal Experts for 22 years, ruled out heart attack as the reason for the death of Judge Loya.
"[29][30] The Congress called it a "It is a sad letter day in India's history," alleging that "the suspicious circumstances in which Loya died, was a matter of deep concern for those who have faith in the judiciary.
Sambit Patra said that Rahul Gandhi should be "ashamed" for his "conspiracy to target Amit Shah, and Indian judiciary, and democracy.
"[33] The Congress, along with leaders of 7 other opposition parties, held press conference to declare their intention of introducing an impeachment motion against Dipak Misra, a first against a sitting Chief Justice of India in history.
[40] Journalist Niranjan Takle wrote a book titled Who Killed Justice Loya which asks many questions regarding the inconsistencies of the case.
Justice Loya could not complete trial of the case — not to speak of reaching to the stage of delivering the judgment — as he died suddenly of cardiac arrest.