A three-judge special bench headed by Justice Arun Mishra said if fixers continue to work and manipulate the judiciary as claimed, neither this institution nor any of "us" will survive.
The bench, also comprising justices R F Nariman and Deepak Gupta, asked lawyer Utsav Singh Bains, who has made claims of a larger conspiracy, to file another affidavit by Thursday morning after he claimed that he has some more "incriminating evidence".
The bench said it will take up the matter for hearing on Thursday.
"We will inquire and go to the root of alleged claims of fixers at work and manipulating the judiciary. If they continue to work then none of us will survive... Fixing has no role to play in the system. We will inquire and take it to the logical end," it said.
The bench also clarified that there is no connection between the hearing of Bains' claims of larger conspiracy and the in-house inquiry ordered into the sexual harassment allegations against the CJI.
Earlier in the day, the apex court directed chiefs of the CBI, IB and Delhi Police to appear and meet in chambers the three judges who are hearing his claim that there was a larger conspiracy to frame the CJI.
The entire episode is "very disturbing" as it concerns the independence of the judiciary in the country, the bench said.
It turned down a fervent request of Attorney General K K Venugopal and Solicitor General Tushar Mehta to order a court-monitored SIT probe into the matter, saying the court was not venturing into any enquiry at this moment.
"It is not an enquiry. We are meeting these officers in secret. We don't want any evidence to be disclosed," the bench said. It had asked the three officers to meet the judges in chamber at 12:30 pm.
After meeting the directors of the Central Bureau of Investigation (CBI) and the Intelligence Bureau (IB), and the Delhi Police commissioner, the bench reassembled at 3 pm to hear the matter at length.
At the outset Bains, who has filed an affidavit in the top court claiming a larger conspiracy of alleged fixers to frame the CJI on allegations of sexual harassment, placed before the bench material to substantiate his claims.
The bench after perusing the material, placed by him in a sealed cover, said "very disturbing" facts have emerged in the matter.
"Can you call some responsible officers from the CBI, preferably the director? Can you call him to meet us in our chambers?" Justice Mishra asked Venugopal.
He replied in the affirmative and referred to the April 20 Facebook post of Bains in which he had claimed that there was a larger conspiracy by some people to fix verdicts of the Supreme Court and malign the office of the CJI.
Mehta told the bench that he was very disturbed with the allegations against the CJI as well as claims made by the lawyer and said they concern the judiciary in the country.
"My submission is that let a special investigation team (SIT) be constituted under the supervision of this court. The truth must come out in the investigation monitored by the court. This will inspire confidence," Mehta said.
Venugopal also supported Mehta's submission and said a thorough enquiry should be conducted in the matter.
However, Justice Mishra said this is a "sensitive issue" and CJI Gogoi has also taken action in the matter.
"This action has been taken by the CJI for the first time in the history of India. This was happening around in the past also but no CJI had the courage to do this," he said, adding that the CJI is taking the action "without any fear".
The bench said full protection should be given to Bains as the court doesn't want evidence to be destroyed or compromised.
At the fag end of the hearing, Bains told the court that he has some more very important and very critical piece of evidence related to the mater and he be allowed to file an additional affidavit.
The bench allowed the request of Bains and said, "It should be handwritten and not typed."
Bains had filed an affidavit following the unprecedented hearing on Saturday during which Justice Gogoi had said that some "bigger force" was behind the controversy as they wanted to "deactivate" the CJI's office and he would not stoop too low even to deny these allegations.
The hearing on April 20 in the case, titled as a matter of "great public importance touching upon the independence of judiciary", was held after stories were published on some news portals about the sexual harassment allegations levelled by a former employee of the apex court against the CJI.