In a small Normandy village, surrounded by wheat fields, Gwen Le Berre keeps a Scientology "electrometer" machine in his bedroom. He opens the large green briefcase and peers at the machine inside. It looks like a lie-detector from an old TV cop show and Le Berre doesn't really understand how it works – he just knows it's a key piece of kit for the Church of Scientology.

Le Berre, 21, keeps the machine as a memento of his mother's life. Four days before Christmas 2006, Gloria Lopez, a 47-year-old secretary, tidied her kitchen, hung out her washing, left her dull, suburban apartment overlooking the railway in Colombes, west of Paris, and walked the 30 metres out on to the tracks. She stood with her arms outstretched, smiling at the driver of the oncoming commuter train. He couldn't stop in time.

Lopez had left Spain in the 80s to marry Pascal Le Berre, a French secondary school teacher. The couple had two children together in Normandy, but divorced soon afterwards. It was just after the split that Lopez – who had always been interested in alternative medicine and esoteric ideas – met some Scientologists and signed up. The church was to become her life. Eventually, she moved to Paris, leaving her two children behind, to be nearer the Scientology Centre.

"When she found herself alone after the divorce, her need for a spiritual search was reawakened," Pascal Le Berre says. "At the start, Scientology gave her confidence, it gave her the illusion she could be stronger than she thought. She saw it as helping the world work better – even a way of saving the world."

Gwen Le Berre had been due to visit his mother to give her her Christmas present two days after she killed herself. His elder sister, Mathilde, had seen her a few weeks before and, although Lopez had lost weight in recent months, she had seemed in good form. They were convinced she would have left a suicide note, and went to her apartment, where the shelves were stacked with Scientology books and DVDs, to search for one. Instead, they found a box of documents in which she had handwritten a series of punishing self-appraisals as part of her membership of the Church of Scientology. She wrote of how she owed money to the organisation for courses, was struggling to advance up the path to spiritual enlightenment, really wanted to succeed as a Scientologist, and regretted every mistake in her life. "She even wrote that she had surfed the internet for two minutes beyond her allocated lunch break at work," Gwen says.

Pascal agrees: "It was as if everything she tried to do was a failure – not advancing up the chain of Scientology courses, but also being distant from her children. She felt a lot of pain over that."

Surprised at the lack of bills and other normal financial documents at the flat – where Lopez often housed Scientologist lodgers, and which other church members regularly visited – the family wondered if other documents had gone missing or been removed.

But after reading her tormented writings, Lopez's children and her ex-husband decided to file a legal complaint against the Church of Scientology for what they claim is its role in her death. They estimate that in around 10 years as a Scientologist, Lopez spent between €200,000 and €250,000 on courses and books – despite her secretary's salary, which was €2,000 a month at the time of her death. Her family also claim that she was counselled by Scientology financial advisers and decided to sell a property she had inherited in Spain, freeing up capital for more courses. "They stole my mother," Gwen says. "I don't feel I knew my mother apart from in her role as a Scientologist."

The police investigation into the Lopez case is just one of a series of investigations and legal cases that has led the Church of Scientology to complain of a "climate of hatred" and a state-sponsored "inquisition" against them in France. Together they have the potential to threaten Scientology's very survival in France and undermine it elsewhere. This autumn, not only could its two flagship centres in France be closed down, but the church itself could be convicted of "organised fraud".

Founded in California in the 50s by the flamboyant science fiction author, L Ron Hubbard, the Church of Scientology claims to offer spiritual self-improvement based on his writings. From the beginning it attracted controversy. It vehemently opposes conventional psychiatry, instead favouring Hubbard's philosophy of mental health, known as Dianetics. This teaches that a person's spirit can be cleared of negative experiences and encourages members to progress up "The Bridge to Total Freedom" through a complex "auditing" process, until they reach the most advanced level of spiritual "clarity". The movement is fiercely protective of copyright over its teachings and its central idea that humans are descended from Thetans – an exiled race from another planet. Hollywood members include Tom Cruise and John Travolta, and Scientology now considers itself to be one of the fastest-growing new religions in the world, claiming more than 7,900 churches, missions and groups in 164 countries.

This year the movement was hit by scandal in Florida when senior members defected and alleged routine physical attacks by the church's leader, David Miscavige – allegations the church denies. But it is France that is threatening to become the organisation's nemesis. Scientology has no religious status in France, and in the 90s it was included in a government inquiry's list of sects. The Church of Scientology says it has six churches and six missions in France, totalling 45,000 members. The French government puts the membership at between 2,000 and 3,000.

Along with the Lopez case, there is an ongoing investigation into a 2008 kidnapping case in which Martine Boublil, a 48-year-old Frenchwoman, is said to have been found being held, half naked, on a vermin-infested mattress in a house in Sardinia. She filed a complaint saying that her brother – an ex-doctor and prominent Scientologist – had kidnapped her, trying to treat her psychological problems himself. The Church of Scientology and Boublil's brother, Claude, denies she was kidnapped and described the case as a "tragic family affair" that the media had sought to exploit.

But this May the most serious fraud trial that the Church of Scientology has faced anywhere in the world opened in Paris. Not only were six important French Scientologists placed in the dock for organised fraud and illegally practising as pharmacists – for selling vitamins classed as medication in France – but, for the first time, the Church itself was accused of organised fraud. In a historic move, the state prosecutor requested that the judges dismantle and dissolve Paris's two flagship Scientology premises: the Celebrity Centre and its bookshop in the capital. The verdict is due at the end of October, and the world is watching. If the Paris centres are shut, it will limit Scientology's operations in France and may have implications elsewhere.

In May, Aude-Claire Malton, a former hotel housekeeper, took the stand against the Church of Scientology at the Palais de Justice in Paris. She described how, depressed after a relationship failed, she met a group of Scientologists at a Metro exit and filled in their personality test questionnaire. A few days later, the Church of Scientology called her to fix an appointment at the Celebrity Centre. "They told me I was in a very uneven state, and that they could help me by giving me some courses." The first course cost €20, but immediately afterwards she was offered a "package" of several sessions for €4,800. She emptied several savings accounts, her life insurance policy, and took out a loan to pay for more courses on the advice of her Scientology personal financial adviser.

Asked by the judge how she could have spent so much, she said: "You have to understand, you're in the brouhaha of the Scientology Centre where everyone repeats to you: 'You must continue, you're making progress, you're going to be able to better yourself, all this is for you.' "

One of the products she spent money on was a full-time 10-day "purification" treatment, where she would take vitamins, then go for a run, then undertake two, three or four hours of sauna. She said she lost four kilos and emerged exhausted. "I had to do it if I wanted to progress," she said.

The judge read out a document described as Malton's Scientology programme: "Move house, get money for life insurance, pay back €16,000, resign." She said the organisation wanted her to work for them at the Celebrity Centre, where she would get courses as part of her pay. They wanted her to move into shared accommodation to cut her costs. But her family and ex-boyfriend stepped in and persuaded her to quit Scientology.

Summing up, the French state prosecutor slammed a "universe of secret rules" and deliberate, planned, fraudulent manoeuvres. She criticised the movement's personality tests and electrometers, which she said were designed to impress and deceive members.

When the verdict is handed down in October, it may not only see the dissolution of Scientology's major Paris branches, but fines of €4m and hefty sentences levelled against six individuals, among them Alain Rosenberg, the director general of Paris's Celebrity Centre and one of the select few Scientologists in France who have attained the church's highest grade of clarity and enlightenment. He denied the prosecution's charges that Scientology was a business that planned to ensnare new members to defraud them. "I'm a man of the church and not a director general of a business," he said. He defined purification treatments, electrometers and courses in Ron Hubbard's book Dianetics as "religious services", arguing that "spiritual elevation" had no price.

Defence lawyers said none of the individuals on trial had made a cent and had acted "out of religious conviction". Scientology's barrister Patrick Maisonneuve argued that while other countries had recognised Scientology as a religion, France was intent on "burning Ron Hubbard's books in the courtyard of the Holy Chapel as the international community watches in horror".

Just before the fraud trial began, pianist and teacher Alain Stoffen stoked the controversy surrounding Scientology in France with his book Voyage To The Heart Of Scientology. It tells the story of his "descent to hell" during more than a decade as a member of the organisation.

A tall, intense man, Stoffen, 48, sits in his modest flat on the edge of Paris and describes an idyllic upbringing in Brussels, during which he decided he wanted to be a musician, performer, composer – "an artist". At 24, he took a piano teaching job in a Paris music school, which he says was run as a recruiting ground by Scientologists. Inspired by the fact that his jazz hero, Chick Corea, was a Scientologist, he plunged into Hubbard's teachings. His initial communication courses at the Celebrity Centre helped Stoffen overcome his shyness and perform better on stage. "The results were phenomenal, tangible, concrete."

He says it's wrong to assume people who join Scientology are "weak". "The people who sign up have a healthy approach, they want to go forward in life, achieve their projects and ambitions." At the Celebrity Centre, he felt he was surrounded by an elite membership from the worlds of art and business. But Stoffen became tortured by his struggle to progress to higher levels of "clarity" and the constant scraping for money to pay for courses. "You would do everything to pay that sum, it was a question of life and death for us, spiritual life or death," he says.

"When you're on the inside, the illusion is perfect. I was convinced that I was thinking for myself, that I became more authentic, that no one ran my life. But the reverse was happening. Without realising, I had been subjected to a real depersonalisation process, a destructuring, so I had become a type of clone. The aim is to destroy, destabilise the person, make them vulnerable, weaken them on a psychological level and place them in a state of dependence."

In 15 years, Stoffen says he spent €45,000 on Scientology courses and books which, he suggests, was not a lot. "Others spent well over €300,000."

He married and had a child with another Scientologist, but after a painful break-up – "managed", he claims, by the organisation – he discovered what he called his secret "personal dossier". It was, he says, 150 pages long and contained minute details of his personal life, the workings of his divorce and custody of his child, and a programme detailing how to "deal" with him and get more money from him. "It was a horrible discovery. I vomited all night." He left in 2001 and filed a legal complaint against the Church of Scientology for extortion, fraud, blackmail and illegally practising as pharmacists. In September 2006, an investigating judge dismissed the case, but in May 2007 that decision was overturned by an appeals court. A judicial investigation has been reopened and Stoffen will meet investigating magistrates in September as he waits for the next step in his case.

"When you leave Scientology, you're totally broken," he says, "as a human being, financially, morally. Your own identity is the result of indoctrination aimed at destroying your critical faculties. When you leave, the feeling of shame and guilt is enormous. It's unbearable."

Agnès Bron, of the French Church of Scientology's public affairs department, says that "false allegations against Scientology with no proof" mainly come from "apostates" who have left the religion, and that the credibility of apostates must be treated with caution. She says Stoffen's "completely deformed image of Scientology" has been used by the media, and the dossier he claims to have discovered had not been secret at all, because all personal dossiers can be consulted by members. For Bron, the Stoffen case, the Paris fraud trial, the Lopez preliminary investigation and other high-profile complaints against Scientology are indicative of "a climate of discrimination" and "orchestrated campaigns" against Scientology in France, pushed by "extremist and antireligious pressure groups". Among those groups she includes the French government agency Miviludes, set up to observe and monitor whether sects and cults break the law or threaten public health.

In a government office attached to the prime minister's residence on Paris's Left Bank, Georges Fenech, magistrate and former MP for president Nicolas Sarkozy's UMP party, sits leafing through his collection of files marked Scientology. As president of Miviludes, Fenech's official mission is to monitor every possible type of behaviour by a sect or cult that might fall outside the law. There are hundreds of small groups being studied from his office, but Fenech is best known as Scientology's number one enemy. In 1997, he was the investigating judge who instructed a major court case against Scientologists in Lyon. A young father, crippled with debts to the organisation, had killed himself by jumping from a 12th-floor window. In court, convictions were obtained for manslaughter and fraud. To Scientologists, Fenech is on a "crusade" against the Church of Scientology, running a sustained press campaign against them and leading a state-sponsored witch-hunt. "It's rather flattering," he smiles. "It proves that the work we do here is efficient."

France, with its republican tradition of the separation of church and state, takes the behaviour of sects and cults seriously – perhaps because it has been shaken by a number of major tragedies in recent history, including the mass suicide of members of the cult Order of the Solar Temple.

But a deep scepticism of sects is not confined to government officials. There was a media outcry in 2004 when Sarkozy, then minister for finance, was suspected of favouring Scientology after his very public meeting with Tom Cruise. Another followed last year when one of his top advisers, Emanuelle Mignon, said the state's attitude to Scientology was questionable. Fenech insists: "Nicolas Sarkozy met Tom Cruise, the international film star, not as the ambassador for Scientology. The meeting was never a question of Scientology." He says the president is "firm" on the issue of sects, and Mignon has given assurances that her comments were taken out of context.

The Church of Scientology argues that secular France is persecuting it for its beliefs as a "new religion". Fenech disagrees. "For France, Scientology is a vast commercial enterprise hiding behind a religious mask," he says. "This is not something against the Ron Hubbardian doctrine, or beliefs about intergalactic happenings thousands of years ago. What we're interested in is that people are dragged into this movement, lose their liberty, autonomy and sometimes their life." He says France protects freedom of religion, "but if a law is being broken, the state will go there. Religion isn't a protection against the law."

Back in Normandy, Gwen Le Berre says he has no interest in any kind of campaign against Scientology – he just wants justice and the truth about his mother. Unable to close the chapter on their grief, the family still pore over what they know of Lopez's life as a Scientologist: how she joined every possible Scientology group in Paris, how she took her eight-year-old daughter to a children's Scientology course and her young son to Scientology summer revision sessions, before her ex-husband insisted she stopped talking to the children about the movement until they were 18. "When she died, I didn't know much about Scientology. It was the last thing that came to mind," her son says. "If, by bringing a case, we can open people's eyes, it will have been worth it."