On Friday a 24-year-old navy medic faces a decision that could lead him to military prison after becoming one of the few conscientious objectors in the Royal Navy since the second world war. That man is my husband, Michael Lyons. He joined the navy in 2005 at 18, as a medical assistant submariner. He chose the medic path because he wanted to help people. In 2008 Michael was promoted to the role of leading medical assistant, and has been very proud of his service to his country for the past five years.

Throughout his navy career he has spent a considerable amount of time hundreds of feet below sea level, thousands of miles away from his home land. Both of us come from military families: my grandfather was a regimental sergeant major in the army and Michael's was a pilot in the RAF. Sadly both died while serving their country.

Last June Michael received an order to deploy for a patrol base in Afghanistan on the 1 March. We were recently engaged and had been planning our wedding for 2011. Michael felt he wanted me to have the legal protection of being his wife, should something happen to him in Afghanistan. So we sacrificed the dream wedding in a beautiful country house that we had booked and married quickly at a register office. We downsized and began to visit family as much as possible before his deployment. All this was done with a sense of duty, knowing that Michael had to go to Afghanistan to serve his country. He was proud.

However, in July this year Michael learned 76,000 military documents had been leaked on the internet and published in analysed form in various newspapers. These documents detailed the military's under-reporting of civilian casualties caused by Nato troops, both in the air and on the ground. Examples included the convoy of US marines apparently driving down a six-mile stretch of highway firing at everyone they saw: 19 unarmed civilians were killed and a further 50 wounded. Closer to home there were the allegations that Royal Marines had shot innocent drivers and motorcyclists on eight separate occasions over a six-month period, and that Ghurkhas had called in an air strike on a family compound, leaving seven innocents dead. These were just some of the reports.

I remember the day I asked Michael how he felt going to Afghanistan, considering the publication of these reports. Upset by what he had read, he said he didn't believe we were over there for the greater good. He went on to tell me he wouldn't be able to live with himself knowing he had been a part of that. He said: "I can't have that on my conscience."

And so it began, the navy mocking the idea he might object to war, the feeling of being ignored, or not being taken seriously. We quickly found the navy's chain of command didn't know how to deal with Michael's fears. He was offered very limited support and advice. And that is not the half of the hell I feel the navy have put my husband through over the last few months.

The navy denied his claim that he was objecting to the war on grounds of conscience, and gave no reason why. He was ordered to see a chaplain, even though Michael is an atheist, and the chaplin's statement implied Michael had a slight political reservation, not a moral objection. If Michael had been dishonest and said he was a committed Christian, and because of his faith he could not be part of war on moral grounds, perhaps this would have been over in an instant. So is the navy saying you cannot have a conscience if you are secular?

The next step was appealing against the navy's decision – within days, Michael had sent off his statement to the Advisory Committee on Conscientious Objectors. In November we received the letter we had been waiting for: his appeal date. And this Friday I can only hope that he will finally be heard.