The conservative pundit and political scientist was speaking at a lecture in Lethbridge, Alta., in February 2013 when he answered an audience question by saying he had "grave doubts" about jailing people who view child pornography, calling it an issue of personal liberty.
Since then, he has apologized and ended his work as a professor with the University of Calgary and as campaign manager for the Wildrose Party.
He also wrote a book.
Persona Non Grata: The Death of Free Speech in the Internet Age tells Flanagan's side of the story and served as a way for him to gain insight and better understand what happened.
"I didn't really understand it," he said. "It happened so quickly ... a few months of study helped me to organize everything in my mind so it was really therapeutic — not in the sense of having a rant but in figuring it out."
Flanagan says what happened next was a "virtual mobbing," an assault on his reputation orchestrated online as people quickly spread and commented on the story.
As reporters began contacting politicians for comment, he says the story quickly morphed from being focused on his comments to being focused on how many people were disowning him.
"It was very hurtful," Flanagan said of the condemnation he received from former friends and allies like Prime Minister Stephen Harper and Wildrose Leader Danielle Smith. "It's all like being caught in a tsunami, you're just trying to stay afloat."
He described the experience as akin to that of Gregor Samsa in Franz Kafka's The Metamorphosis, when Samsa wakes one day and without explanation, finds himself transformed into a monstrous, insect-like creature repulsing everyone around him.
Flanagan returns fire at 'vindictive' Harper
One line in the book has prompted speculation that Flanagan could be trying to get back at Harper for disowning him.
In it, he writes that Harper can be "suspicious, secretive, vindictive — falling into white-hot rage over meaningless trivia, other times falling into week-long depressions in which he's incapable of making decisions."
However, Flanagan says he put it in the book because it's an essential part of the story, in which top politicians "threw the first stones and touched off a nation-wide mobbing" of him.
Understanding their motivation for disowning him so powerfully was key in telling his side of the story, Flanagan said.
"The only way that I can explain the language that the [Prime Minister's Office] used was some degree of payback in there, because the Prime Minister never forgave me for writing an earlier book, Harper's Team ... I don't think we ever spoke again after that and he's got a long memory so these factors do come in to what happened, so I had to mention that."
Flanagan goes on to describe the "dark, Nixonian" character he says lies within Harper, which leads him into unnecessary conflicts, but also praises the "brilliant characteristics" which first drew Flanagan to work for him.
Overall, Flanagan says the experience has made him reflect on his career and some of the problems with modern-day politics.
"Maybe it's poetic justice," he said of his history levelling attacks against politicians as a commentator. "These all-out assaults on people, I really don't want to be a part of that. I see it happening from all parties, doing it against each other. Well I guess they signed up to play. But sometimes then they do it against private citizens who never even wanted to be on the field.
"I really don't want to be a part of that an more, even as a political commentator. I would like to deal with issues and strategies and so forth, but not with persons."