Like many teenage boys, Rhys Morgan loves video games, rock music and hanging around with his friends. He works hard at school and tries to do his bit helping out at home. But what makes this 17-year-old a little different is that he also finds time to join battle with powerful, wealthy organisations that promote miracle alternative cures for serious diseases.

Morgan's burgeoning campaign, run from the front room of his family's house in a cul-de-sac in Cardiff, is gaining him friends and enemies. He is winning plaudits from within the sceptical community and from some journalists impressed at his gumption, but is berated by those desperate to believe in the treatments offered – and has spent countless hours in recent weeks batting away threats of legal action.

So why does this floppy-haired teenager bother? Wouldn't it be less hassle to focus on becoming even better at Team Fortress 2 or just kicking back and listening to his favourite bands, Muse and Radiohead?

"It can be nerve-wracking but I think that getting the message out there is a lot more important than me being sued," says Morgan. "I think there's a need for more people to speak out. I hate the idea of anyone being taken for a ride."

Morgan was not always a sceptic. His mother, Dawn, reveals that he believed in Father Christmas until he was 11 when she and his father, Paul, had to break the bad news. "I think they should have told me a little earlier," Morgan says. As a young boy he went to church with his grandparents, only becoming an atheist after attending a Christian camp. "I had a good time but a few weeks later stopped believing. I'm not quite sure how that happened."

Morgan's first contact with online scepticism dates to his early teens when he became interested in Snopes.com, a website devoted to debunking urban legends. Then he wrote an essay for his English language GCSE expressing doubts about the validity of many alternative medicines. This interest in medicine did not emerge out of nowhere: his father is an intensive care doctor, his mother a nurse.

But it was when Morgan was diagnosed with a serious illness – Crohn's disease – that he plunged deep into the world of scepticism. While off school last year, he set about researching the disease and was alarmed at some of the "miracle cures" on offer. One particularly grabbed his attention: Miracle Mineral Solution (MMS), which is described on its website as the "answer" to Aids, hepatitis A, B and C, malaria, herpes, TB and "most cancer".

Morgan looked into MMS and was alarmed to find that the US Food and Drug Administration (FDA) had warned that, when used as directed, the solution produced was "a potent bleach" and urged anyone using it to stop immediately and throw it away. Similar warnings have been issued in this country.

"A few people on support forums seemed to be pushing MMS on others. I started telling people on the forums, look, this treatment doesn't seem to be that great." He got "kicked off" one forum. "They told me I was being rude and inflammatory by questioning other people's choices."

Happily for Morgan, he went into remission at the start of this year (thanks to "conventional" drugs prescribed on the NHS, he is keen to emphasise). He returned to school and continued his studies. The teenager found he now had two groups of friends – his Cardiff pals and online colleagues from the increasingly well-organised sceptical community. The two groups do not overlap and Morgan says his local friends do not know much about his online activities. "I think they'd be bored by it. I don't tell them much about it all."

In this year's summer holidays, Morgan's eye was caught by a campaign aiming to raise money to send a young woman with inoperable brain cancer to a centre called the Burzynski clinic in Houston, Texas (motto: Tomorrow's cancer treatment today). The clinic says it uses "antineoplastons" – "molecular switches that turn off life processes in abnormal cells" – to treat cancer patients.

Morgan did some digging into the clinic and was not convinced. "I couldn't find anything substantial on the internet to support what was being claimed." He says he was angry at the idea of desperate people spending what could be the last days of their lives flying across the globe and putting their faith in what he believes are "unproven" treatments. He posted a blog about the clinic and again got on with his life and studies.

But at the start of November an email dropped in Morgan's inbox from one Marc Stephens, who accused him of libelling the Burzynski clinic.

"I was a little bit scared. I didn't know who this guy was," says Morgan. He told his mum and dad and asked for advice from fellow sceptics and sympathetic lawyers. Further emails followed. Morgan was worried that if he lost a libel case, his parents' assets, their house, cars and savings could be at risk.

It got even heavier. Stephens told Morgan he would contact his school about his activities and, most disturbingly, included a satellite view of the Morgan family home in one message.

"It was extremely odd. It was as if he was saying: 'I know where you live.'"

It was a tense time for the Morgans. When a suspicious brown package arrived addressed to "Dr Rhys Morgan", his mother was so worried about what it might contain that she thought it best to open it outside. It turned out to be a wristband sent by a friend.

Morgan went on the attack. He published the email exchanges on his blog and asked pointed questions about Stephens' legal credentials.

At the end of last month the clinic issued a press release distancing itself from Stephens. It said he had been hired as an "independent contractor" to "provide web optimisation services and to attempt to stop the dissemination of false and inaccurate information". It accepted that sending a Google map and making personal comments to bloggers had not been appropriate. The clinic apologised and said it "no longer has a professional relationship" with Stephens.

The press release does not name Morgan but says that bloggers who had made "false and defamatory" statements would be contacted by its lawyers. It also claims that the woman whose fund-raising campaign attracted Morgan's attention is doing well and that her tumour is shrinking. The press release goes on to list 13 articles that it said had been published since 2006 supporting antineoplaston therapy.

Morgan is unbowed. He believes he is right and will not back down. "It's quite clear that they are trying to intimidate me, silence me. Science should be settled through more papers and better understanding of the world as opposed to through lawsuits."

He is not a fan of the libel laws in the UK. "They favour the person making the claims of libel very heavily. People can be sued for things published in academic journals. That can't be right."

Morgan now plans to delve into the work of a second cancer clinic and is also interested in tackling other alternative medicines and beauty products.

When he leaves school he plans to go to university and then become a doctor and journalist. On his Twitter page, he already describes himself as "Journalist. Skeptic." He thinks he'll be able to juggle all his callings.

So what does he believe in? Morgan does not hesitate: "Evidence-based medicine. If evidence can support something, I'm all for it. One thing that really gets me is when people claim sceptics have closed minds. That's not true: a true sceptic will be convinced by evidence. And even if the evidence supported the most absurd claims, the sceptic would agree that it's true."