Jennifer Dennis studied her 13-year-old son's skin and was uncertain which to be more astonished by: the shape made by the strange dots running the length of his forearm, or how they got there.

"When I looked at it, the shape was definitely a cross, like a Christian cross," said Dennis. "Zach said his teacher did it with an instrument that gave off something like a lightning bolt. It was red, like a sunburn or if you burn your arm on the oven."

The next morning, Dennis was standing in the reception of Mount Vernon middle school demanding to know what had been done to Zachary.

That was three years ago and the small, deeply religious Ohio town is bracing itself for the answer to Dennis's question after the lengthy de facto trial of a man who is either a decorated teacher martyred for his Christian faith, or a religious zealot who spent years undermining the very science he was paid to teach.

Along the way, the dispute has prompted Bible-waving students to march on their school, set teacher against teacher, and forced Jennifer Dennis and her family to leave town.

At the heart of the controversy is John Freshwater, who taught at Mount Vernon middle school for 21 years.

Freshwater said he had done the same science experiment to hundreds of students before Zachary Dennis, using a Tesla coil, which gives off an electric spark.

The teacher said it was painless and harmless – although a doctor would later testify that Dennis had second-degree burns – and that he had made an X, not a cross, on the boy's skin.

That might have been the end of the matter after the school ordered Freshwater to stop using the coil on children.

But Zachary Dennis's parents asked him what else was going on in science class. Out poured accounts of lessons on evolution mingled with creationist theories about "intelligent design", a euphemism for the hand of God, of questions about religious beliefs and of classroom walls pasted with the Ten Commandments.

Other children told of also having crosses burned on their arms.

The school sacked Freshwater in June 2008. He invoked his right to a hearing that is about to reach its conclusion after dragging on and off for more than a year and costing the school board close to $500,000 (£300,000).

Dick Hoppe – a former nuclear missile engineer who later helped design the Apollo spacecraft command module, and who was more recently a visiting professor of biology at a local college – has attended almost every day of the hearings.

"One student, when asked what he had learned about science from Mr Freshwater, testified that what he learned was you can't trust science. That surprised me. I didn't want to believe it was that overt," said the avowed atheist.

"Freshwater was teaching what the text taught – age of the Earth, fossils – and then would add an overlay of creationist material that cast doubt on what the text said. He would use a handout that described all the adaptations of a woodpecker and at the bottom he added: was intelligent design involved? He was teaching against the curriculum."

The hearings heard that Freshwater pinned up a poster of President George Bush and the then US secretary of state, Colin Powell, at prayer, and another advertising an evangelical meeting.

The school also discovered questionnaires in which Freshwater asked students whether religion was important to them.

Bonnie Schutte, a science teacher in the adjacent high school who received students from Freshwater's class, told the hearing that when she asked new pupils what they had previously learned, some said that science is "a lot of theory and guesswork" and that "evolution follows opinion and it's not fact".

Freshwater denied responsibility for writing references to God and religion on class notes even though the hearings were told that they matched his handwriting.

But he did acknowledge that in 2003 he was ordered by school officials to cease a part of his teaching in which he scattered Lego blocks on a table and said that however long you left them there they would not build themselves, and so something as complex as the eye could not be the result of evolution but had to have been created by someone.

All this was known to some other teachers who kept their own children away from Freshwater's class, but failed to alert the school board or other parents.

While the school board would appear to have a commanding case, Freshwater and his supporters managed to persuade a large part of the town, on the edge of the Appalachia region, popularly regarded as culturally backward and home to about three dozen churches and an evangelical university, that the issue is about his religious rights.

The teacher allied himself with a militant rightwing group, the Minutemen, and held a rally in Mount Vernon's town square at which he announced he had been sacked for refusing to remove a Bible from his desk.

The school denied that was the motive but the claim prompted a wave of support. Students held a "take a Bible to school" day and wore T-shirts proclaiming that God supported Freshwater.

"We have a Christian martyrdom thing going here. This town is ripe for it," said Hoppe. "My guess is that a majority in this town believe that man was created in his present form in the last 10,000 years, the creationist view. You've got a large conservative fundamentalist population."

Freshwater declines to speak to reporters on the advice of his lawyers but he has alleged that members of the school board have been out to get him since he made a proposal in 2003 for the science curriculum to include intelligent design.

The teacher is a member of the Trinity Worship Centre, part of the country's largest Pentecostal denomination, where the pastor, Don Matolyak, is in effect Freshwater's spokesman.

"We heard many times: if he'd had a Qur'an on his desk he would never have had a problem. They're probably right because that would be seen as diversity," said Matolyak, who has stood in as a teacher for Freshwater's class.

"This is about a person's religious liberty. I see this as a battle that's going on in America, and there are those who want to totally secularise America and almost explain away our Christian heritage."

Hoppe, whose wife has taught at the school for 35 years, says that Freshwater was not alone in pressing his religious views on his pupils.

"There's been a small group of teachers who've been running what amounts to a private Christian school within the middle school. There is testimony from several teachers about how they also had Bibles on their desks and religious displays," he said.

Many in Mount Vernon have sided with Freshwater. Persuaded that the Dennises were hounding the teacher over nothing more than a Bible on his desk, some turned on the family.

Jennifer Dennis said: "We've gotten phone calls, things in the mail, anonymous letters. They send scriptures and how you should raise your children, implying we're not raising our children correctly. Everywhere we go I feel like people know it's us so they don't talk to us or they will say things. Even in church." Eventually it was too much for the Dennis family. They moved 35 miles away.

Targeting schools

Creationists have long fought to force "intelligent design" on to the school curriculum. They first tried to use legislatures in states where the Christian right is strong, but those moves were defeated by political opposition or in the courts. Now activists are trying to take control of school boards. Missouri is the latest state to consider a law that would require the teaching of the "scientific strengths and weaknesses of the theory of … evolution" – interpreted as intended to give equal weight to creationism.

In other states such as Mississippi and Alabama, efforts to force the teaching of alternative views to evolution have foundered. But creationists have had more success through election to school boards, particularly in Texas, where the Christian right has succeeded in limiting the teaching of evolution in biology lessons. It is now pressing for history lessons to emphasise the part played by Christianity in the founding of the US.