The first episode of S-Town, the new seven-part podcast from the team behind Serial, begins with producer Brian Reed talking about “witness marks” – the nearly invisible traces that are left on the guts and gears of antique clocks by each repair: “I only learned about all this because an antique clock restorer contacted me and asked me to help him solve a murder.”

It all started with an email. A man named John B McLemore sent a note to the general email address of the podcast This American Life, with the subject line “John B McLemore lives in Shit Town, Alabama”. Reed, a producer on the show, scanned the email and decided to take it to the editorial team, even though he wasn’t exactly sure what the story was, other than a small-town resident with a large vocabulary complaining that the scion of a wealthy family was bragging that he got away with murder. He invited This American Life’s producers to come investigate for themselves.

Producer Brian Reed recording S-Town. Photograph: Andrea Morales

“There was something about the tone,” says Reed. “His weird punctuation and capitalisation – and then what he was saying.” The team decided that it was worth at least a phone call. After speaking with McLemore, Reed was intrigued. “This guy was funny and dark and wanted me to know about him,” says Reed. “He was like: come see this giant maze I built in my backyard! He also sent me some reading on Bibb county – not a history of the area or its coal industry, but a copy of A Rose for Emily by William Faulkner.”

S-Town’s executive producer, Serial co-creator Julie Snyder, agreed that McLemore was something special. “Brian played me 20 minutes of their first phone conversation, and it seemed very promising that there was a story, even though I had no idea what the hell it was going to be,” says Snyder, laughing. Eventually Reed took McLemore up on the offer, heading down to Alabama to see what this “shit town” (abbreviated to S-Town for the podcast’s title) was all about.

The podcast documents the results of that visit and the friendship that unfurled between Reed and McLemore, a tattooed and nipple-pierced manifesto writer with a worldwide reputation as an antiquarian horologist. What starts out as a murder mystery ends up taking listeners into the heart of a deeply intelligent and troubled man, and the small town he begrudgingly calls home. “It seemed like something you would read about in a novel,” says Reed. “This accomplished clock restorer juxtaposed with the portrait of this decaying town.”

Reed and Snyder started reporting the story almost three years ago, which was before Serial helped kickstart the podcast boom. “We were still working on Serial when Brian told me about it,” says Snyder. “I remember saying that maybe this could be a Serial type of thing, but at the time I didn’t even know what the hell Serial was going to be. I figured we could always do it on the weekend if Serial crashed and burned.” Serial, of course, turned into a massive hit, downloaded more than 250 million times, and podcasts became the format of choice for long-form serialised storytelling, which worked perfectly for S-Town. “We always thought this would be an experiment in storytelling,” says Reed. “The podcast format would free us to do things that we couldn’t pull off on the radio.”

Warning: the remainder of this article contains spoilers for S-Town.

Brian Reed records his voiceover. Photograph: Sandy Honig

Reed determined that the rumours of a brazen murder and an equally shameless cover-up were not true, and he and Snyder tried to figure out if they needed to move on – This American Life kill about 50% of their stories, according to Reed. But something happened that made them keep going.

The third episode starts with the shocking news that McLemore has killed himself in a gruesome manner, leaving his mother alone, his friends with no answers, and his reportedly extensive estate in complete disarray. “When John killed himself, it was a shock to the system,” says Reed. Ever the reporter, Reed recorded the phone call where he got the news of McLemore’s death, and it’s searing to listen to him cry over his lost friend. “It was really hard to edit that,” says Reed. “It was a long time before I could bring myself to listen to any of the tape with John in it. Luckily, I didn’t need to, because there was a lot of reporting to do before I had to delve back into it.”

The S-Town team. L-R: Julie Snyder, Ira Glass, Brian Reed and Sarah Koenig. Photograph: Sandy Honig

Snyder says: “I felt so bad for Brian. When he called me to tell me it was like his friend died, we weren’t talking about it like a story. This is where [executive producer] Ira Glass is very helpful, because Ira has a tendency to move on a little more quickly than the rest of us. He was the one who pointed out that this made it a story.”

In the wake of McLemore’s death, Reed returned to Alabama. “It seemed like stuff was happening and we would figure it out later,” says Snyder. The podcast was no longer a portrait of a man but the portrait of his absence, and the complications left in his wake. “Just jump into its world,” says Snyder. “It’s very specific and hermetic and intimate.”

While Snyder is eager to get to work on the next show from Serial Productions (and yes, there is a third season of Serial in the works), after spending three years on a story, Reed isn’t quite ready to leave yet. “I have this document – a document that I didn’t know I was making – of the last year and a half of his life,” says Reed. “I’m worried that after this comes out and I’m not working on this that I’m really going to feel this dearth of John in my life. I’ll really feel like he’s gone. At least I’m getting to spend time with him now, making sense of it and trying to explain it to other people. That’s going to be glaringly absent in a few weeks.”

• S-Town is available to download on 28 March