Jones is notorious for saying the 2012
Brokaw's appearance was clearly an attempt to assuage the Sandy Hook families who were outraged and even threatened legal action against NBC News.
Jones, a radio host who operates the right-wing website Infowars, repeated his theory in the interview. Kelly said he never disavowed his previous statements in their conversations and noted there was no evidence to back his claims.
Kelly interviewed Newtown parent Neil Heslin, who described the devastating loss of his son.
"I think he's blessed to have his children to spend the day with, to speak to," Heslin said. "I don't have that."
Kelly did have several heated exchanges with Jones, who was sweating profusely during their sit-down. She opened by pressing him on why he called the victims of the terrorist bombing at an Ariana Grande concert in Manchester, England, "liberal trendies" when many were pre-teen girls.
Jones tried to rationalize his statements in the interview but for the most part seemed frustrated by Kelly's queries.
In a live-streamed video aired on his YouTube channel, Jones reacted angrily to the final taped "Sunday Night" piece as it aired. He lambasted Kelly and the mainstream media.
"This is a giant, evil misrepresentation," he said. "They continue to misrepresent what I've said and what I've done."
Still, he declared victory — popping a bottle of champagne and angrily vowing to keep up the fight against "globalism" and the lies covered up by the mainstream media.
On social media, reaction was mostly predictable.
Media colleagues and critics generally gave Kelly high marks for the toughness of the piece, which disputed nearly every theory Jones has promoted through Infowars.
Far-right commentators repeatedly called the interview a "hit piece."
The rigor of the piece will likely take some of the sting out of critiques of Kelly, some of which suggested that her transition from Fox News to NBC News was off to a rocky start.
On Twitter, ABC News legal analyst Dan Abrams said: "Watching @megynkelly interview with Alex Jones, I'm even more convinced that her piece wasn't just ok to do, but important journalism."
Media Matters, an ardent critic of Kelly during her Fox News days, believed public pressure made it a tougher segment.
Still, there was concern that Kelly had provided a larger platform for Jones, who despite a large following that includes
Washington Post media columnist Margaret Sullivan wrote on Twitter: "Bottom line on NBC's Alex Jones piece: Strong editing gave it an edge & made him look like a kook. Still a win for him; boosts his profile."
NBC News will now have to hope that the positive reaction is enough to reverse some of the damage to Kelly and its brand after the weeklong drubbing. The Nielsen ratings, out on Monday, will help determine whether it was worth it.
Some advertisers asked not to air during "Sunday Night," which is not uncommon when news programs present provocative topics. NBC News also did Kelly no favors by previewing clips of her interview with Jones in a way that made it appear to be less than a critical grilling.
Jones, likely sensing that NBC was going to toughen up the segment, had already sought to undermine Kelly by leaking taped phone conversations in which she assured him it was not going to be "a hit piece."
NBC News has stood firm on airing the Jones interview, despite the blowback. Executives have said Jones' large following and political influence make him newsworthy no matter how despicable his views may be. Kelly addressed the controversy at the top of the program.
"Some thought we shouldn't broadcast this interview because his baseless allegations aren't just offensive, they're dangerous," she said. "But here's the thing: Alex Jones isn't going away. Over the years, his YouTube channel has racked up 1.3 billion views. He has millions of listeners and the ear of our current president."
But the network's own TV station in Connecticut, which serves the Newtown area, decided Friday not to air the program after complaints from its employees and viewers in the area. One former NBC News producer speaking on the condition of anonymity called the move "unprecedented."
"Sunday Night" was developed as a platform to launch Kelly as one of the network's signature stars, as prime-time newsmagazines built around a single anchor have been a rarity on network TV in recent years. Kelly was signed by NBC earlier this year after becoming a prime-time star at Fox News.
Now she is being subjected to greater scrutiny as her new program airing 7 p.m. Sundays on NBC's broadcast network is up against CBS' "60 Minutes," which remains the most popular news program on TV after 49 seasons.
After a competitive ratings showing in its premiere with an interview with Russian President Vladimir Putin, "Sunday Night" dropped 42% in its second week on June 11 to 3.6 million viewers, less than half of what its CBS competition delivered.
"Sunday Night" is airing through the summer and will vacate the schedule for NBC's NFL prime-time broadcasts. But in the fall, Kelly will host a new daily daytime program that follows NBC's "Today," where attracting a largely female audience is crucial. Causing pain to grieving parents with the Jones interview likely was not going to help her connect with those viewers.