The R Document occurs during a future time in the United States when crime, especially violent crime, has become so extreme a problem that FBI Director Vernon T. Tynan is promoting an especially drastic solution: a Thirty-Fifth Article Of Amendment to the Constitution of the United States that would allow the Bill of Rights to be suspended in favor of its provisions during a national domestic crisis.
The protagonist of the novel is Attorney General Christopher Collins, whom Wallace modeled on Ramsey Clark, who, while in that office, became one of Hoover's bitterest enemies.
At the time when the novel begins, his predecessor, former United States Army Colonel Noah Baxter, is ill, and indeed dying, from a stroke he had suffered.
This extortion, which fails, owes to an attempt that hard-core delinquents had made, years ago, to stop an anti-drug crusade which the priest had been conducting by entrapping him for drug dealing.
On the set of the program, which a certain Brant Vanbrugh moderates, Collins is embroiled in a debate with Tony Pierce, who had resigned from the FBI after throwing his support to FBI Special Agents that Tynan was manhandling (who themselves had also resigned from the Tynan Bureau as a direct result) and now heads a grassroots organization called DBR, or Defenders of the Bill of Rights, which he has organized to stop the 35th.
To do that without involving President Wadsworth, Tynan seeks out money (from illegal campaign contributions) from Donald Radenbaugh, an attorney whom Baxter considered one of his few friends and confidants, who has been confined in Lewisburg Prison since being wrongly convicted of extortion.
Radenbaugh then tells Collins about Page 1 of The R Document, explaining that Tynan had conceived the 35th Amendment by examining communities with low crime rates in hopes of recommending anti-crime legislation to Wadsworth and the Congress, and finding "company towns" to have the lowest crime rates, and Argo City, Arizona, owned by Argo Smelting And Mining, where the Bill of Rights had been effectively suspended, to have the best long-time record.
As it proves, under Page 2 of The R Document, Tynan would actually personally create the national crisis that the 35th, once ratified, would need to be invoked by ordering the President of the United States assassinated, thereby giving the Attorney General grounds to suspend the Bill of Rights.
The novel ends with grounds for hope, as the President agrees to pardon the wrongly-convicted Radenbaugh, then forms a commission (including Collins and Pierce as members) to clean Tynan's evil influence out of the FBI and overhaul it; after that, he promises to discuss, with Collins, a comprehensive program of economic and social legislation which will be intended to solve the problem of crime, the original problem that had actually led Tynan to hatch his plot in the first place.
However, as it accused the American government of being run secretly, from behind the scenes, by an evil, tyrannical cabal and completely negated Wallace's own civil-libertarian arguments, he publicly disowned it.