Loya had allegedly died of cardiac arrest in Nagpur on December 1, 2014 when he had gone to attend the wedding of a colleague's daughter.
A bench comprising Chief Justice Dipak Misra and Justices A M Khanwilkar and D Y Chandrachud had on March 16 reserved the judgement on the pleas.
The Maharashtra government had argued in the apex court that all pleas seeking an independent probe into Loya's death were motivated and aimed at targeting "one individual" in the guise of upholding the rule of law.
It had come down heavily on alleged accusations, bullying and browbeating of judges in the top court by some activist lawyers in the Loya case and said that the judiciary and judicial officers need to be saved from such averments.
Meanwhile, those seeking an independent probe into the matter had referred to the sequence of events to highlight that a fair investigation was needed to rule out any foul play in the death.
The issue of Loya's death had come under spotlight in November last year after media reports quoting his sister had fuelled suspicion about the circumstances surrounding it and its link to the Sohrabuddin case. But Loya's son had on January 14 said in Mumbai that his father had died of natural causes.
In the Sohrabuddin Sheikh fake encounter case, BJP President Amit Shah along with Rajasthan Home Minister Gulabchand Kataria, Rajasthan-based businessman Vimal Patni, former Gujarat police chief P C Pande, Additional Director General of Police Geeta Johri and Gujarat police officers Abhay Chudasama and N K Amin have already been discharged.
Several accused, including police personnel, are currently facing trial for their involvement in the alleged fake encounter of Sohrabuddin Shaikh, his wife Kausar Bi and their associate Tulsiram Prajapati in Gujarat in November 2005. The case was later transferred to CBI and the trial shifted to Mumbai.
A batch of pleas, including those filed by Congress leader Tehseen Poonawala and Maharashtra-based B S Lone, was filed in the top court seeking an independent probe into Loya's death in 2014.
Four senior-most apex court judges -- Justices J Chelameswar, Ranjan Gogoi, M B Lokur and Kurian Joseph -- at their January 12 press conference had questioned the manner in which sensitive cases were being allocated and Loya's case was one of them.