In connection with his multi-year research and publications on Louis Riel, Flanagan published a reinterpretation of the North-West Rebellion, defending the federal government's response to Métis land claims.

[5] As part of his political activism, Flanagan began to write as a columnist in 1997 in The Globe and Mail, National Post, Calgary Herald, Ottawa Citizen, Maclean's, and Time.

[9] Since the 1970s Tom Flanagan published numerous scholarly studies "debunking the heroism of Métis icon Louis Riel, arguing against native land claims, and calling for an end to aboriginal rights.

[12] Flanagan has written about his change of views regarding Métis leader Louis Riel: I had earlier accepted that the Métis had serious unresolved grievances; the government of Canada never gave a satisfactory response to the complaints; that Riel resorted to violence only after legal means of action had failed; and that he received a trial of questionable validity before being executed by vengeful government.

As I sifted the evidence this became less and less convincing to me until I concluded that the opposite was closer to the truth: that the Métis grievances were at least partly of their own making; that the government was on the verge of resolving them when the Rebellion broke out; that Riel's resort to arms could not be explained by the failure of constitutional agitation and that he received a surprisingly fair trial.

[17] In connection with this work, Flanagan also published a reinterpretation of the North-West Rebellion, highlighting how the government had responded to Métis land claims.

Belanger questioned why Flanagan as a professional academic did not access more robust peer-reviewed scholarly resources regarding analysis and statistics, preferring instead to make extensive use of newspaper clippings from the Calgary Herald, the National Post, and The Globe and Mail and the conservative magazine the Alberta Report.

Flanagan did not visit any First Nation communities to research the publication nor did he quote any Aboriginal leader in support land privatization in exchange for the end of the reserve system (Belanger 2002:107).

He claimed he echoed "the assimilation rhetoric of 19th century policy makers and politicians" which perpetuates a stereotyped image of First Nations as "uncivilized" and "unwilling to shake the social pathologies he suggests proliferate all reserve communities."

[21] Pamela Palmater, a Mi'kmaq lawyer who holds a new chair in indigenous governance at Toronto Metropolitan University, argued in her review that First Nations?

Second Thoughts provides a summary of Flanagan's convictions that "since First Nations in Canada are uncivilized and their governments produce 'wasteful, destructive, familistic factionalism,' they should not be entitled to self-governing powers, special tax exemptions or federal funding, but should be assimilated and their reserves divided up into parcels of individually owned, 'fee simple' lands available for sale to non-aboriginal people and corporations.

"[23] In order to become self-supporting and get beyond the social pathologies that are ruining their communities, aboriginal people need to acquire the skills and attitudes that bring success in a liberal society, political democracy, and market economy.

According to Suzanne Methot's review of the book, Flanagan claimed that "European civilization was several thousand years more advanced than the aboriginal cultures of North America" and colonization was therefore "inevitable" and "justifiable.

[30] Boutilier said that their criticisms of the First Nations Land Management Act (FNLMA) which he calls a "quiet success", are "quite simply inaccurate", and that the authors, while acknowledging the FNLMA’s "effectiveness in reducing transaction costs", would leave "each First Nation on its own to develop its own system of property rights and failed "to provide technical assistance in the form of model land codes and zoning regulations.

[44] In Victor Buffalo, the Samson Cree band, located near Hobbema, Alberta, unsuccessfully challenged the federal government's implementation of Treaty Six.

[48] Flanagan adopts the philosophical analysis of John Locke and Emer de Vattel that European colonization of North America by Western civilization was justifiable and inevitable.

[49][e] He asserts that "European civilization was several thousand years more advanced than the Aboriginal cultures of North America both in technology and social organization" (Flanagan 2000:6).

[50] Dimitri Soudas, spokesman to Prime Minister Stephen Harper, decried Flanagan's comments and said the former Tory strategist "should be charged with incitement to commit murder."

[51] Ralph Goodale, deputy leader of the Liberal Party in the House of Commons, called Flanagan's remarks "clearly contrary to the Canadian Charter of Rights and Freedoms.

Flanagan responded, then made a "side-bar" comment: "But that's actually another interesting debate or seminar: what's wrong with child pornography, in the sense that they're just pictures?

"[53] Flanagan says no one complained or criticized his comment, and maintains that he used the phrase "just pictures" to shock students into questioning pre-held ideas, which is the job of a teacher.

The University of Manitoba Aboriginal Students' Association wrote a letter of complaint to the head of the political studies department, George MacLean, but Flanagan's comments did not receive widespread attention.

Danielle Smith, who was mentored by Flanagan, and served as Wildrose Party leader in 2009, cut her ties with him saying "there is no language strong enough to condemn [his] comments".

(Ted) Morton, Rainer Knopff and history professor David Bercuson[47][48][62] who are strongly committed to strategic and direct influence on public affairs with a long-term vision.

The Calgary School of political science – Barry Cooper, Ted Morton, Rainer Knopff and I, along with our historian outrider David Bercuson – did not cause this transformation, but we and our students have played an honourable part in making it happen.

"[47] Tom Flanagan joined the right-wing populist Reform Party of Canada in 1990[63] and began working there in 1991 as director of policy research.

Two prominent conservatives present the case for more representative government"[66] which argued that the Liberal Party only retained power through a dysfunctional political system and a divided opposition.

The authors called for an alliance of Canada's conservative parties, and suggested that meaningful political change might require electoral reforms such as proportional representation.

"Our Benign Dictatorship" also commended Conrad Black's purchase of the Southam newspaper chain, arguing that his stewardship would provide for a "pluralistic" editorial view to counter the "monolithically liberal and feminist" approach of the previous management.

In response, the federal government passed the Manitoba Act, which carved the province out of the sprawling region called the Northwest Territories and established Canadian dominion.