Vajpayee, who had delivered a provocative speech in Ayodhya a day before the December 6 demolition, called the incident "unfortunate". He claimed that he and other senior BJP leaders had tried to "prevent it" but "did not succeed".
Roy persevered. Why had they not succeeded, he asked in his easy, languid tone. Vajpayee blamed a section of kar sevaks but eventually conceded that a solemn assurance to the Supreme Court had been broken.
"We are sorry," Vajpayee said.
New Delhi Television (NDTV), the venture Roy had started with wife Radhika in 1988, was not yet a full-fledged channel then. Roy's trademark beard was still black.
Over the next quarter century, NDTV provided content and then launched India's first private 24x7 English news channel, turning a group of young men and women into some of Indian news television's best-known faces.
The channel went through crises and controversies, the loss of top anchors and of ratings, but survived.
But on Monday, the couple who had pioneered private news television in India appeared more vulnerable than ever. The CBI raided the Roys' Greater Kailash home over allegations that they had defaulted on the repayment of an ICICI bank loan worth around Rs 500 crore.
NDTV has denied the charges. The CBI insists it has a strong "prima facie" case.
But independently of the merits of the charges against the Roys, the raids have sent a chilling message to many journalists across news platforms in India, sparking fears that NDTV's criticism of some of the government's policies may have played a role.
Roy's journey so far has been the story of the evolution of private television news in India. The future of that journey, many worry, may equally determine the path others take going forward.
Roy hails from a family of boxers - his father was known by the nickname "Hurricane" while others carried names like "Typhoon" and "Tempest". His journey in television hasn't been without fights.
He started out by analysing elections on Doordarshan in the mid-1980s before launching NDTV. Months after he interviewed Vajpayee in December 1992, he entered into talks with Rupert Murdoch. Former Doordarshan director-general Ratikant Basu, who was Murdoch's point man in India, mediated their talks.
Over the next few years, the Roys broadcasted news through STAR TV, Murdoch's project that beamed private news programmes into India for the first time, from the safety of Hong Kong.
But just as Vajpayee's rise in those years had initially been unsteady, his first government lasting all of 13 days in 1996, the Roys encountered tumult too.
In 1998, as Vajpayee, the BJP's first Prime Minister, began six years of rule, the Roys broke with Murdoch to launch their own 24x7 channel that would remain unrivalled in the private English news space in India for several years.
The channel launched popular faces like Barkha Dutt, Rajdeep Sardesai and Arnab Goswami. Some of them left for other channels that over time began garnering higher viewership than NDTV 24x7.
But Roy remained, in the words of author Anil Dharkar who profiled the anchor for a 2011 book called Icons, the "overriding patriarch" of Indian news television. Through it all, according to Dharkar's account, Roy's wife Radhika - whose sister Brinda Karat is a CPM politburo member -stood by him, even if from behind the scenes.
"When he comes on air, Radhika Roy is known to monitor his performance carefully," Dharkar wrote in Icons.
"He wears an ear plug through which she tells him to straighten his tie or not repeat a certain remark, if he has ended up saying something untoward. Theirs is one of the most enduring teams in television history."
NDTV - and Roy - have faced criticism and controversy earlier too.
Critics had accused the channel of discarding ethics after it chose not to act against Dutt, a star anchor, when tapes following the 2009 general election suggested she may have carried messages between politicians to assist the formation of a Congress-led coalition government.
More recently, on November 8, 2015, Roy found his credibility as an election analyst under severe scrutiny. An NDTV exit poll for the just concluded Bihar elections had suggested a comfortable BJP victory. Instead, the Rashtriya Janata Dal-Janata Dal United-Congress combine had steamrollered into power.
Worse, Roy and NDTV had projected a BJP win just as the first counting trends had begun arriving in the morning. "Let me start with an explanation and an apology," Roy said that evening.
Roy has not shied away from showcasing his proximity to power in the past, either. In 2013, NDTV celebrated 25 years as an independent channel at Rashtrapati Bhavan -- the only time an Indian President has allowed his residence to be turned into a venue for a business celebration.
But, through the churning and the criticism, the Roys survived. And the legacy of private television news in India that they had started continued to explode in the form of new channels, now increasingly broadcasting a raucous cacophony that invades Indian living rooms each evening.
On Monday, though, when NDTV journalists arrived at their principal office in Greater Kailash - a five-minute walk from the Roys' home - the mood was sombre. The Roys weren't around.
An NDTV reporter recounted how the staff worked warily, wondering if and when the CBI would also enter their studios and workstations. The CBI didn't come to their office. But a chill different to the one in December 1992 had set in.