In the early hours of 2 May 1973, Assata Shakur was stopped on the New Jersey Turnpike by a state trooper named James Harper, allegedly for driving with a faulty rearlight. In the car with Shakur were fellow Black Liberation Army (BLA) members Zayd Malik Shakur and Sundiata Acoli. In a second patrol car was Trooper Werner Foerster. Minutes after they pulled over, both Zayd Malik Shakur and Trooper Foerster were dead, and Assata and Trooper Harper were shot and wounded. In 1977, Shakur was convicted on one murder charge and six assault charges and sentenced to life in prison. She escaped in 1979 with the assistance of BLA members posing as visitors, and has been a fugitive ever since. Last year, the FBI placed the 66-year-old on its list of the top 10 most-wanted terrorists.

This month, Assata: An Autobiography is being republished by Zed Books. In the foreword, iconic black activist Angela Davis describes Shakur as a "compassionate human being with an unswerving commitment to justice". She says the FBI is simply trying "to frighten people who are involved in struggles today". In a television interview she gave last year, Davis was clear that "Assata is not a threat. She is innocent," adding that the case was emblematic of the police brutality and racism that she and her peers suffered. "Forty years seems as if it were a long time ago; however, at the beginning of the 21st century, we're still dealing with the very same issues – police violence, healthcare, education, people in prison and so forth. People really don't know the details and are not aware of the extent to which [Shakur] was targeted by the FBI and the COINTEL programme."

How did Shakur become a woman considered so dangerous by the US government that her name is ranked alongside members of Hezbollah? There is a $2m reward for information on her, unprecedented for an American citizen who maintains her innocence and has become a hip-hop cause célèbre, cited in songs by everyone from Public Enemy (Rebel Without A Pause) to Common (A Song for Assata). Undoubtedly, her relationship to Tupac– she was his step-aunt and godmother – has played a role. But it is only a small part of a story tangled in a series of criminal charges – which were variously dismissed, acquitted, or ruled mistrial – of violence, prison time, escape and political asylum in Cuba.

Life in the US in the 50s was tough if you weren't white. The civil rights movement was slowly trying to undo centuries of damage and change government policy, but there is no doubt that as a black child born in the 1940s, Shakur's life was permeated by racism in a way that seems almost unimaginable today. Born JoAnne Deborah Byron in Queens, New York, she moved with her grandparents from New York to Wilmington, North Carolina, to live in the house that her grandfather had grown up in. It was a time of segregation, of "Coloured Only" and "White Only" signs, and Jim Crow laws. As a result of the prejudice shown, Shakur's grandparents drilled into her the idea of personal dignity. "I want that head held up high, and I don't want you taking no mess from anybody, you understand? Don't you let me hear about anybody walking over my grandbaby."

Respect was currency, and understandably for a black family in the south, to be held on to at all costs. Her grandparents forbade her to look down at her shoes or make subservient gestures when talking to white people. "No 'yes, ma'am' or 'yes, sir'", she writes. "I was told to … hold my head up high, or risk having my grandparents knock it off my shoulders."

For all of her awareness of systemic and institutionalised injustice in the US, politicisation came somewhat late to Shakur. She dropped out of high school, leaving her mother's house to get a job. She ended up in New York working one of those "dingy, boring $95-a-week jobs. I was one of those slaves where you pay a fifth of your salary for taxes, some more for social security, another $5 a month for union dues, and the rest was not even enough to die on." She and her friend Bonnie would go to a bar on Broadway called the West End, and there she made friends with some African students. They told her about curried chicken and groundnut stew. Then one day in 1964, a discussion on the roots of the Vietnam war changed her life. "I never forgot that day. We're taught at such an early age to be against communists, yet most of us don't have the faintest idea what communism is. Only a fool lets somebody else tell him who his enemy is."

The reward poster provided by the New Jersey state police for Shakur's capture. Photograph: Associated Press

Shakur changed her name in 1971. "The name JoAnne began to irk my nerves," she writes in her autobiography. "I had changed a lot and moved to a different beat. I didn't feel like no JoAnne, or no Negro, or no amerikan. I felt like an African woman. My mind, heart, and soul had gone back to Africa but my name was still stranded in Europe somewhere."

From 1971 to 1973, Shakur was alleged to have committed a series of audacious crimes, sometimes alongside other members of the BLA: two bank robberies in New York, the kidnap and murder of a drug dealer, armed robbery (during which she was shot), and the attempted murder of policemen in an ambush. She was either acquitted or the cases dismissed. Then came the events of 2 May 1973, in which Trooper Foerster and Zayd Malik Shakur were killed. In her autobiography, Shakur details the conditions in which she was kept during the days that followed – her food was spat in, she was not allowed to contact a lawyer, and Zayd Malik's dead body was left lying next to her. She recalls some compassion from a German nurse at the hospital, who protested about the tightness of the cuff on Shakur's ankle and covered it in gauze, and later showed her the call button so she could buzz the nurses' station for help.

It was in hospital that she first met Lennox Hinds, the national director of the National Conference of Black Lawyers. "In the history of New Jersey, no woman pretrial detainee or prisoner has ever been treated as she was, continuously confined in a men's prison, under 24-hour surveillance, without adequate medical attention and exercise," he says. Shakur's defence team filed a civil suit against the state, charging that her conditions were cruel and inhuman (she was held for more than a year in solitary confinement, in the basement of the Middlesex county jail for men). She ascribed to all her conditions a unifying theme: the smell. "I don't care what jail I've been in, they all stink. They have a smell unlike any smell on earth. Like blood and sweat and feet and open sores and, if misery has a smell, like misery."

In January 1977, after years of incarceration, the case was brought before a judge and jury in New Jersey. There is much evidence to suggest the trial was not fair: transcripts of the jury selection show at least two of the jurors expressed prejudice before the start of the trial. There was evidence that the offices of the defence team were being bugged, and materials relating to her case that went missing from the home of her late lawyer Stanley Cohen were later found with the New York City police. Hinds called the trial "a legal lynching and a kangaroo court". The defence could not get an expert witness to testify. As Shakur noted: "It was obvious I didn't have one chance in a million of receiving any kind of justice." She testified holding on to a photo of her daughter (conceived with fellow BLA member Kamau Sadiki while they were both in jail, and born in 1974). The jury reached a verdict after 24 hours – she was found guilty on all seven counts. As Hinds explained: "Under New Jersey law, if a person's presence at the scene of a crime can be construed as 'aiding and abetting' the crime, that person can be convicted of the substantive crime itself." Shakur was handed a mandatory life sentence.

According to FBI special agent Barbara Woodruff, Shakur's ranking on the FBI's Most Wanted Terrorists list was simply a way to get more public attention. "This case is 40 years old so there may be people who don't know anything about it. On the 40th anniversary, we are trying to bring the public's attention to the case. I don't think it's extreme to have her on this list," she says. "Back in the 70s when the BLA were more active, they were looked at as part of an internal security investigation that eventually would have morphed into domestic security or domestic terrorism. You have to look at the history of the BLA. Even though she was convicted of one murder, she was part of an organisation which, from the 1970s to 1984, were involved in at least 38 criminal incidents, including armed assaults, assassinations, bombings, hijackings – of those 38, 18 were against law enforcement officers."

Shakur's radicalisation can be traced back to her time at college in the mid-60s, where she became involved with the Golden Drums society, a black activism organisation. She cut off her "conk" hairstyle and grew her hair naturally in an afro. In 1970, she fled to California after a failed marriage, and worked as a doctor's assistant, volunteering at Alcatraz during the time it was taken over by Native Americans who were protesting about broken treaties and exploitation by the US government. "I will never forget the quiet confidence as they went about their lives calmly, even though they were under the constant threat of invasion by the FBI and US military," she writes. "They had many of the same problems we had: education, organising the people to struggle and raising consciousness. They damn sure had the same enemy, and they were doing as bad as we were, if not worse."

A chance meeting with members of the Red Guard – a radical Chinese-American youth organisation – made her aware of how unrevolutionary her life was. "If I wanted to call myself a revolutionary I was going to have to earn the title. Revolution is about change, and the first place the change begins is in yourself."

Shakur is escorted from Middlesex county jail, November 1973. Photograph: New York Daily News Archive

Shakur joined the Black Panther Party in New York on her return from California in 1970. "Panthers didn't try to sound all intellectual … They simply called a pig a pig." Shakur also felt that they truly understood what and who they were fighting. "One of the most important things the Party did was to make it really clear who the enemy was: not the white people, but the capitalistic, imperialistic oppressors."

But she became disillusioned shortly after joining, taking issue with the political education (PE) programme in the party. "With a few exceptions, PE classes for Party members turned out to be just the opposite. The basic problem stemmed from the fact that the BPP had no systematic approach to political education. They were reading from the Red Book but didn't know who Harriet Tubman, Marcus Garvey and Nat Turner were. A whole lot of them barely understood any kind of history, black, African or otherwise." She was further discouraged by founder-member Huey Newton's status within the party. "When Huey changed his title from defence minister to the ridiculous-sounding "Supreme Commander", and then to the even more ridiculous "Supreme Servant", damn near nobody said a word. That was one of the big problems in the Party. Criticism and self-criticism were not encouraged, and the little that was given was not taken seriously."

Sensing her expulsion was on its way, she quit the BPP, leaving behind her close friend Zayd Malik Shakur. All the while, she believed her apartment was bugged by the FBI. "Everywhere I went it seemed like I would turn around to find two detectives following behind me. I would look out my window and there, in the middle of Harlem, in front of my house, would be two white men sitting and reading the newspaper. I was scared to death to talk in my own house. When I wanted to say something that was not public information I turned the record player up real loud so that the buggers would have a hard time hearing."

She began the life of a traveller and around this time joined the BLA. In an opening statement she delivered to the courtroom during one trial in 1975, she said: "The Black Liberation Army is not an organisation: it goes beyond that. It is a concept, a people's movement, an idea. The concept of the BLA arose because of the political, social, and economic oppression of black people in this country. And where there is oppression, there will be resistance. The BLA is part of that resistance movement. The Black Liberation Army stands for freedom and justice for all people."

In his book Target Blue, author Robert Daley described Shakur as the "soul" of the BLA, the "mother hen that kept them fighting and kept them moving". Shakur discounts the book as "sensationalism, groundless accusations and outright lies". But the BLA broke up in the early 80s and is now just a footnote in the history of militant black organisations, with no fewer than 13 former BLA members currently in jail.

Assata: An Autobiography, by Assata Shakur is available now from Zed Books, priced £8.99. There will be a launch event for the book at the Black Cultural Archives, in Brixton, London on August 21st at 7pm. www.bcaheritage.org.uk