While the report labels the state - under a succession of apartheid, National Party governments - the "primary perpetrator" of torture, assault, murder and assassination from 1960-1994, it accuses Mr Botha of leading the state "into the realms of criminality" after he took power in the late 1970s.
Previous governments had murdered opponents but a line was still drawn between those considered a danger to the state and those critical of it. But during Mr Botha's reign, the TRC says, all activists and critics became hit squad targets.
The TRC rejects claims by former members of the powerful State Security Council, which was chaired by Mr Botha and included cabinet ministers such as FW de Klerk, did not know that the state was sanctioning murder.
Chief Mangosuthu Buthelezi, leader of the Zulu Inkatha Freedom Party (IFP), who, like Mr Botha, refused to ask the TRC for amnesty in return for a full disclosure of the truth, was also guilty of atrocities, along with senior members of his party. The TRC said it had made a mistake in not forcing him before the commission after he and his party boycotted proceedings.
Like many of the TRC's findings, the conclusions on Chief Buthelezi are inconvenient to post-democracy political alliances.
It is Chief Buthelezi who steps in as acting head of state when President Nelson Mandela and his deputy, Thabo Mbeki, are abroad, part of the ANC's attempts to woo the IFP, once its bitter enemy, into an alliance.
The report concludes there is "overwhelming evidence" that the IFP was the primary non-state perpetrator of apartheid violence, responsible for a third of all violations - including 4,500 killings - reported to the commission.
It also accused the IFP of working with the apartheid regime to create hit squads which targeted anyone - primarily the ANC - opposed to the government or Inkatha.
President Mandela's former wife, Winnie, was also implicated in murder, attempted murder, assault and abduction.
In a chapter devoted to two weeks of TRC hearings during which she was accused of the assaults and at least a dozen murders and attempted murders - along with her infamous band of thugs, the Mandela United Football Club - the TRC concludes that she initiated and took part in the assault of teenage activist Stompie Seipei Moeketsi, who was later murdered by the team coach, Jerry Richardson.
Most explosive is the TRC's rejection of the alibi Mrs Mandela gave at Stompie's murder trial.
She claimed she was hundreds of miles away in Brandfort when the boy was murdered. The TRC report says she was in fact at home in Soweto where the assaults on Stompie, who she had accused of being an informer, took place.
The TRC report implicates her in other murders and assaults, and criticises the ANC for not doing more to curb her and her club, a charge which has angered the party. MrsMandela also did not apply for amnesty.
The TRC report yesterday recommended that all perpetrators who did not take up the offer of amnesty and indemnity from future prosecution in return for truth, should now be pursued with zeal in the criminal and civil courts.
One page was blanked out in the report following the success of former president FW de Klerk in having findings implicating him in state-sponsored terrorism removed (at least temporarily).
It was this which seemed to propel the ANC into court in a similar action. Elsewhere, Mr de Klerk was criticised for his "evasiveness" during party submissions to the TRC.
But while individuals were singled out, "white indifference" and "hostility" to the commission were highlighted. The TRC hearings were a largely black affair. Few whites attended, despite appeals by the TRC chairman, Archbishop Desmond Tutu.
The commission said that members of the old regime's establishment had hedged and obfuscated. Few had "grasped the olive branch" of amnesty for disclosure.
When former leaders took responsibility for the past their apologies seemed no more than "ritualised platitudes" and "there was no real appreciation of the enormity of the violations of which these leaders ... were accused, or the massive degree of hurt and pain their actions had caused".
Both President Mandela and the archbishop paid tribute to the 21,000 victims who came forward with their appalling stories of inhumanity and brutality. Considered by the TRC as central to the process, every victim was named in the report.
The TRC attacked the media, business, church and the judiciary for support and complicity with apartheid. A tax on business, one of the chief beneficiaries of apartheid, was among the ideas for funding reparations for victims.