Quinn relishes standing on his balcony after rain and the smell of it through the holes in the tall sandstone escarpment that backs his house. His smell has returned and that triggers a flood of other memories. His slow but, in medical terms, ground-breaking rehabilitation has taught him to no longer reach out for those memories but to wait for them to come to him.

Only photographs and a meticulously kept diary are there to remind him of what took place over the past four years. He still looks in wonder at snaps of a lengthy family holiday to the United States and Europe in 2012 of which he has no recollection. He is beginning to run again through the adjoining national park where, five decades ago, Skippy was filmed. To a frustratingly small extent he is beginning to taste his food.

His 16-year-old son Callum and daughter Caitlin, 14 - the two who willed his return to Sydney - now spend alternate weeks living with their father. To Quinn, the two teenagers, their height and their accompanying electronic devices, still seem miraculously transformed from the pre-adolescents he last fully remembers.

Recently a former Greater Western Sydney colleague now working at the Western Bulldogs told Quinn that Tom Boyd had spoken with great appreciation of the dietary help given to the AFL rookie by the pioneering sport scientist. Quinn looks forward to the day he can actually remember working with Boyd. He wishes he could remember the succession of weddings at which he was master of ceremonies.

Most of all he wishes he could remember his farewell to his beloved father-in-law or the eulogy he delivered at his Hobart funeral. But recently he recalled a moment afterwards when his former wife, Natlee, took his hand outside the church. He said he was learning to let go of Natlee and their life together but he holds on to that recollection.

John Quinn has agreed to open up at this time about his still rare but increasingly prevalent illness - an illness initially misdiagnosed and which led to him for some weeks being institutionalised into a psychiatric ward at Sydney's Hornsby Hospital - because for him the true happy ending to this ordeal takes place on Monday.

Quinn's new life has him operating each day with a large heavy diary, his lap top, his IPad and IPhone. All four are repeatedly cross-checked but there is no cross-checking required for this coming Monday, April 20. This is the day he returns to work for the GWS, the day the doctors initially believed would never come with  Quinn and his illness and subsequent recovery the subject of two international medical studies.

John Quinn, for 10 years the highly respected high-performance boss at Essendon, Australian track-and-field coach and most recently founding head of sport science at the AFL's youngest club, has not worked at GWS since the day back in November 2013 that his perplexed head of football, Graeme Allan, suggested he take a break and seek medical help.

It was "Gubby'' Allan who would two months later, in January 2014, find Quinn wandering lost and delusional around the football club's car park and who called the GWS doctor Joe Lombardo insisting he be immediately hospitalised. And who, according to what Quinn has been told, he would abuse for not visiting him in hospital even though Allan, along with Kevin Sheedy, did so regularly. "I never thought I was going to die," said Quinn before adding with his customary dry delivery: "But even if I did I couldn't remember."

There had been frightening times. he said. for his children. "One day we were driving along and I saw truck carrying hay bales. 'We're going to the circus', I told them. 'We're going to follow this truck all the way.' I'd head out for a meeting in Canberra and just as likely turn and head for Newcastle."

Allan was one who bore the brunt of Quinn's increasingly strange behaviour, heightened emotions, memory loss and rapid mood swings as the 2013 season progressed. Like so many close to Quinn, his work colleagues believed he was suffering from an emotional breakdown as a result of his marriage break-up. The day of the car park incident Quinn had called Allan for help, saying he had lost his car after having taken training with Mark "Choco" Williams. Except there had been no training that day and Williams had left the club almost 17 months earlier.

At hospital he was initially diagnosed with depression and placed on heavy anti-depressive medication. Not only did his family refuse to believe that he was clinically depressed but nor did many friends and medical colleagues. His close friend from Essendon, Dr Bruce Reid, at one stage called his attending physician to insist the man he had worked with for more than a decade had never shown depressive tendencies.

A new series of tests at the end of January 2014 provided the breakthrough Quinn's family desperately yearned for and probably saved him from the permanent damage that the fits and convulsions Quinn was suffering would have caused. Quinn was diagnosed with Limbic Encephalitis, an auto-immune disease that  had affected his brain and led to the short-term memory loss and strangely heightened emotions. Quinn had lesions on both sides of his brain.

The medical world is still learning about the unusual strain of encephalitis, which can be caused by tumours but also by severe stress. Auto-immune diseases, said Quinn, are the fastest growing in the world and increasingly prevalent among young women. But the diagnosis explained all the missed meetings during Quinn's last full season with GWS, the times he got lost, the intensified feelings of love and hate, the overreactions to humour and sadness and the times he would fly off the handle. And why, on Christmas Day 2013, when he headed from Sydney to Canberra to see his family, he called them from Yass to say he was headed to Melbourne for an important meeting with Bruce Reid.

Quinn's sister Rosemary Holder and his 83-year-old father Noel convinced him to wait at a cafe in Yass so they could meet him for a quick catch-up. "We broke land-speed records to get there," said Rosemary this week. "He had kidded everybody for months because he would set his destination on his GPS to stop himself from getting lost."

Added Rosemary later in our conversation of her brother's recovery over the long months he lived with her and her husband at their Canberra home: "It was very difficult to watch him go from the dynamic, fast-paced man to being like a four-year-old child."

In practical terms, according to Quinn, the smartest decision he made in hindsight was as a 20-year-old when he took out an income-protection policy. The Giants continued to pay him for many months until his policy kicked in but he said he would forever appreciate the football family and the various small and large acts of kindness that started  from the AFL's head office.

"The hardest part is not that I lost my job or my work," he said, "because I have never worked a day in my life. My work is my lifestyle and I lost my lifestyle. It's not so much that I want to repay the club but I want to be able to do something great for them.

"I want to give them something they don't expect. I want to revolutionise the way we identify talent. I want to set new goals for young athletes in western Sydney and Canberra and regional New South Wales. And I will always appreciate what they have done for me. What they and the AFL have done for me during this. I know he gets a bad rap at times, but from Andrew Demetriou, who I know supported me, down. I just so appreciate that they supported me through this.

"I'm told there's eight per cent of my memory that might never come back, but I'll take that. This might be as good as it gets, but I'll take it. I'll take sitting here having a coffee with you even if it means the odd tear."

Despite the heartbreak that accompanied the break-up of his marriage in early 2013 and the lingering pain, it was when the subject of his elder sister Rosemary came up that Quinn's eyes first filled with tears. Some football stalwarts would be surprised to learn that another name that  provokes emotion is that of  Allan, the Giants' head of football, who has stayed in constant touch and now marked out a program for Quinn's new part-time role heading up the Giants' academy.

Quinn cries less these days than he did at the height of his treatment but the spontaneous tears are a legacy of "the disease", as he calls it, and the subsequent heavy cortisone medication that has significantly decreased. Now at least he knows when they are coming.

Rosemary, who remains adamant she should not be portrayed as the hero of this story, equates witnessing Quinn departing her Canberra home to move back to Sydney to "watching your first child heading into his first day of school". Rosemary was Quinn's primary carer for most of 2014 after she and her father realised they would have to reshape their lives for him.

Quinn moved to St Ives and shared his home initially with a family friend, the young soccer player Bryan Bran, formerly of South Melbourne, who had returned home with a misdiagnosed injury from a club in Amsterdam. Quinn trained Bran and Bran looked after Quinn, acting as his chauffeur and all-round helper. Every three weeks he still undergoes intravenous immunoglobulin, a blood plasma transfer to maintain his status quo.

Quinn understands he can no longer run the Giants' sport science program. It would be selfish of him, he said, to push for his old job back. But apart from overseeing the club's academy and mentoring coach Jason Saddington, he plans to return to study for his PhD. He already holds a masters in occupational health and safety and has put forward to the GWS a proposal to work with club sponsors by implementing wellness programs into their workplaces.

It is six months since Quinn moved back to Sydney, five months since he regained his driver's licence and one year since I wrote a form of tribute piece I believed would be my last column about Quinn.

To sum up, the high-performance boss came to the AFL from athletics, where he had been the head track and field coach for the Tasmanian Institute of Sport. He was lured to Essendon by Kevin Sheedy in 1998 and oversaw the Bombers' fitness regime and more - the highlight being their near-perfect 2000 season. Quinn remained at Essendon after Sheedy left but could not work in harmony with his successor Matthew Knights. He joined Sheedy at the Giants in 2010 as the fledgling club's founding head of sport science, moving his young family from Melbourne.

Former Bomber, Port Adelaide's Angus Monfries, recalls: "He was my first-ever fitness coach when I arrived at Essendon as a 17-year-old. To me, Quinny was a lot more than just a fitness coach, I felt like he genuinely cared about you as a person and was interested in how you were going off the field. Back then there wasn't the sort of support-welfare people employed like today and for me, being away from family and friends, Quinny was someone I felt comfortable chatting with if I had any issues.

"He would always open his family up and invite players over for dinner, but I also felt that he was a coach that was always good at getting the best out of yourself on field and in training. He had a great knack of, however you were feeling physically, to give that little bit more." The troubled Andrew Lovett had lived with Quinn's family when he was at Essendon and briefly again late last year.

Monfries was one of almost 150 who in early January this year attended Quinn's 50th birthday party at Greater Western Sydney's main function room. Twelve months after being hospitalised, Quinn delivered a self-described motivational speech and then cut a ceremonial ribbon placed in the centre of the room with large gold scissors declaring he was cutting his ties with the past. He told guests he would hold them all to account, asking all to write on a small piece of paper provided what they hoped to achieve over the next three years. He has kept every one of those.

The guest list included Giants boss Dave Matthews, Allan, assistant coach Luke Power and a number of former Bombers, including Jason Johnson and Damien Peverill along with Bruce Reid, whom sister Rosemary said willingly took her worried calls about Quinn even on the day before - she later learnt - he was to front the AFL Commission hearing over his role in the Essendon supplements scandal.

Said Monfries: "He was the same John Quinn and was well on his way to recovery. It was a great night and it shows with the amount of people that flew in from interstate the sort of person Quinny is and how highly people think of him."

One highlight of the night was the roast delivered by Graeme Allan, who said it was by instruction that he make fun of Quinn and his previous strange behaviour, only to then watch sheepishly while others delivered heartfelt and emotional speeches. And the biggest highlight according to all of the above was young Caitlin Quinn, the 14-year-old who was told last year she was unlikely to ever adequately converse, let alone live with, her father again. Caitlin sang Leonard Cohen's Hallelujah.