A determined Jack Charlton marches across the lobby. He's got something to say. "Could've done with you tonight." It's a few hours after Ireland's dismal 0–0 draw with Egypt in Palermo and Liam Brady is sharing a drink with his ex-teammates. The same ex-teammates who couldn't find the moment of inspiration to produce even a meaningful attack against the African side.

Brady would have.

"Only when you were at your best, mind," Charlton adds, returning to Brady's table a few minutes later. The extra detail was unnecessary. And unfair.

But then, if you're looking for injustices from Brady's career, take your pick. There's the travesty that arguably Ireland's greatest ever footballer just missed out on Ireland's greatest ever football moments. There's also the fact he never got to play on such a platform at all. Then there were all those scandalous refereeing decisions that ensured that fact. Most of all though, there was the manner in which Charlton ended his career at the highest level. He hauled Brady off in the first half of a friendly with West Germany to prove a point to the public that, surprisingly, he didn't have the courage to make in private.

Of all the distraught Irish faces when so many decisions had gone against the side, Brady's was the most globally recognised. And the sight of him trudging off that day was set to become the enduring image of another controversy: the debate over whether Charlton was sacrificing purism for progress. Was the country too willing to sell its soccer soul? That issue became the single great caveat to all of Charlton's conquests.

To an awful lot of people though – and some extent Brady himself – much of that is empty talk. There was, after all, another great injustice to his time in the game: the fact he had so much ability compared to almost everyone else. It gave him a career that was, if not Ireland's most glorious in terms of medals, certainly the most glamorous.

That he never got to play in a tournament befitting his talent doesn't necessarily bother him. But some of the reasons do. Brady has been involved in five very questionable refereeing controversies with Ireland, four as a player, three in Paris. Sitting in the Merrion Hotel about to analyse the 2010 World Cup for RTÉ and with that Thierry Henry handball fresh in the memory, Brady is convinced they're part of the same continuum. All conditioned to ensure the little guy loses out. Does he actually believe there were outright conspiracies when he was a player?

"Oh yeah. Without any doubt. We didn't have anything going for us as far as Fifa were concerned. We were really just also-rans and in referees' eyes as well – that referees could do things to us and there'd be no repercussions. Whereas, if it was England or a bigger nation there'd be such an outcry or maybe investigations they wouldn't take that chance. But with us it happened. No doubt about that... Certainly now, looking back, I feel very strong that there was a lot of skulduggery going on."

For Argentina 78, Ireland had goals disallowed in knife-edge games away to both France and Belgium, "under circumstances that were strange to say the least". The Spain 82 qualifiers under Eoin Hand (right) then brought another trip to Paris, another undeserved 2–0 defeat and another controversy.

"That game would have tipped the group in our favour. But, 1–0 down, Kevin Moran scores a legitimate goal. Disallowed. Absolutely robbed there again."

Yet, Ireland were still in a strong position. Cyprus were seen off 6–0 and qualification really was in sight. It might finally, actually happen. Ireland in a major championship. A point in the next game in Belgium could have done it. In fact, a point absolutely would have done it. The way Ireland played they deserved much more. What they certainly didn't deserve was a series of incidents that made the entire Henry scandal look like no more than a simple sleight of hand.

Lightning and relentless rain almost caused the match to be abandoned. But the real storm started just before half-time. Ireland had been awarded a free-kick on the right. Brady flicked it on, Stapleton finished. It was a move that had come off many times at Highbury.

"Frank and I had a relationship having grown up at Arsenal and knew each other very well. With a free-kick I would wait for Frank to walk a yard like he wasn't interested, then he was going to come back and I just put it in where he was going to arrive. I knew he was onside because we knew each other so well he would never be offside."

The linesman apparently didn't think so either. As Brady says, "there was a lull". Then a whistle. Referee Raul Nazare had disallowed the goal before, a full three seconds later, the linesman guiltily put his flag up.

And still, it gets worse. Three minutes from the end of the game, Belgian captain Eric Gerets is launched into the air even though he's a good foot away from the nearest Irishman. Rene Vandereycken's free-kick bounces off the bar for Jan Ceulemans to react decisively. Belgium got the win that ultimately took them to the World Cup. Nazare got a lot of abuse. First Mickey Walsh, familiar with the Portuguese referee from his time at FC Porto, called him a "cheat". Hand went further. "You're a disgrace. You've been paid off. You've robbed us." Brady, meanwhile, asked Walsh the Portuguese word for thief and put it to Nazare's face. Was that real rage, or actual restraint?

"Well you can very nearly get banned totally from football when the likes of that happen. You'd have to stop yourself attacking the referee coming off the pitch. The sense of anger is, well... but it was really, really diabolical. I have a theory Fifa would prefer some teams to get to World Cups because of major sponsorships or money. And well it all came out that Belgium was a totally corrupt federation. Anderlecht had a title taken off them, there was the Uefa Cup game against Notts Forest. I reckon we were done in France and Belgium – we were hijacked. And then to lose out on goal difference shows we were good enough to qualify."

The 'what-ifs' for Ireland began to evaporate soon after Brussels though, as Brady freely admits. Instead, there were a lot of 'what-nexts?' All the dubious refereeing decisions couldn't explain some of Hand's. A very decent man whom the players all had time for, it became clear he wasn't really ready for the job. Hand's inexperience, having only ever managed Limerick, started to engulf him and he struggled to deal with both the deficiencies of his squad and the association that employed him.

"He suffered more than John [Giles] the pantomime that the FAI was at the time. Whereas before we would maybe take the piss, now we were getting disgruntled and Eoin couldn't handle it. He didn't have the power or the bottle or the self-assurance to take on the FAI."

Worse though was when Hand let the media see just how much they affected him. Mick McCarthy had come under constant criticism during the 1986 World Cup campaign for his lack of pace. Hand's defence of his player, however, only led to John O'Shea of the Evening Press betting he could beat the centre-half in a 50-metre sprint. Incredibly, Hand accepted and managed to coerce McCarthy into competing: "Nah, nah, that's going to cost me 50 quid if you don't race." Contrary to the myth, it was O'Shea – and not McCarthy – who pulled up after the Yorkshireman won a first race. But a subsequent injury was blamed on Hand's bet.

"You see when you work with a top, top manager he doesn't listen to that. But in those days it was 'Look at what he's written now'. Instead of Eoin completely ignoring John O'Shea, he got involved in it. I mean I don't even see Trapattoni reading newspapers. He'd know the guys to see but he doesn't know what they write or who they write for. Doesn't give a monkey's. That kind of confidence transmits to the players. But with Eoin it was transmitting bad vibes because he was getting upset about what they were writing. He was bringing more pressure by showing this. He wasn't a confident man and that was transmitted to the team."

Brady's own independent spirit, however, was an ingredient that would eventually prove unpalatable to a manager as controlling as Charlton.

"My first impressions were, 'this is not going to last between myself and himself'. We weren't that enamoured. John had been in the running for the job as well and I wanted him and we got Jack in unusual circumstances," Brady chuckles. That would become a theme.

"It was amateurish in many ways. He was a person who could be laughed at because he was so disorganised.

"To Jack the job was a salary. Then he began to understand the Irish, what a great people we are. They looked after him in a manner he couldn't believe."

First though, Charlton had to get the players to believe in his way. Or, if they didn't want to believe, just go along with it. Brady forced himself but was never content with the compromise.

"John had a belief over how he wanted the team to play from the back through midfield, passing the ball around. And that's a way of playing that appeals to every player. Jack was taught in the FA at that time, brought up by a guy called Charles Hughes. And his theory was that the more times you get the ball in the box, the more goals you score. Get possession of the ball in their half by pressurising, getting throw-ins, getting corner-kicks... that leads to goals."

Which was always going to be a problem for a player who prized passing.

"He couldn't leave me out because I was playing well but I probably didn't do myself any favours. I couldn't change the way I played. The ball would come to me and I'd do what came naturally – dribble, maybe, in midfield. If I did it successfully nothing was said. If I didn't I'd have people roaring at me from the sideline but I just ignored it. I accepted that I had to go along with what he wanted for the most part, yet I didn't toe the line completely. It was that bit of rebellion that wouldn't allow me do it totally his way."

But, little by little, a balance was struck between the two philosophies for the betterment of the team. "I think he figured out that the good outweighed the bad and I had a bit of a licence to play the way I wanted to play but I did adapt my game a bit then. I went far less back to receive the ball because I knew, one, he would be unhappy with me, two, he'd give a bollocking to the centre-half who gave it to me. That was where the modifying of the way I played came into it."

Brady is also keen to stress that there were aspects of Charlton's style that were universally beneficial.

"First of all, Jack had plenty of self-confidence. That assurance Eoin didn't... Second, the foundation was correct with Jack. Having been a defender, he would single out their best player and make sure we stifled him which was always good in a coach. He was also good at free-kicks, corner-kicks. We weren't giving away any stupid goals. Things that Trapattoni has introduced in many ways now. And, like Trapattoni and Giles and all good managers, Charlton had a knack of building team spirit."

With all the talk of the famous camaraderie of the squad, Gordon Strachan's infamous line is put to Brady, that "team spirit is an illusion created in victory".

"Strachan's talking rubbish there. Team spirit is what leads to victory. Okay, team spirit might be fortified by victory. But team spirit is the manager getting through to every one of his players that 100 per cent workrate is required no matter what position you're in, no matter who you are. All the best managers can get that out of their players. Giles had it. Trapattoni has it. Charlton certainly had it at the time.

"I always got on with Jack on a personal level, played cards together, laughed together. But there was this difference of philosophy. I would argue if we had Giles at the same time he would have done it in a more attractive and pleasing fashion. That never left me so there was always that suspicion of one another."

That potential problem finally played out very publicly in a September 1989 friendly. Up against West Germany, it wasn't to such blue-chip opposition Charlton wanted to make his point. Brady had barely played in the Italia 90 qualifiers because of injury so Charlton wanted to show the player as well as those calling for his reinstatement that he couldn't provide the industry Ireland's set-up required... by hauling him off after 33 minutes. That sight has been held up as the defining image of Charlton's approach – the blunt manager derisively discarding the country's most nuanced player. On reflection now though, even Brady admits that interpretation is a little too simple.

"I was 33, had a serious cruciate tear. Maybe wasn't able to do what I'd done prior to qualifying for Euro 88. But, rather than Jack saying to me, 'Liam, I really need somebody that maybe has more legs', he went out of his way to create this thing against Germany. The more success Jack got, the more bolshie he got... if Jack hadn't qualified for '88 he might have been coming around to the players, 'What do you think we should do?' But '88 went well, we all came home in an open-top bus and he got bolshie. What happened in '89 – he was probably feeling he could do whatever he wanted. But I knew my time was up."

Brady was selected for one more game – a send-off against Finland. That and the meeting in the Palermo hotel show how he and Charlton had, to some degree, repaired their personal relationship. In any case, he found Italia 90 almost as rewarding as a co-commentator for ITV. For that fifth penalty against Romania, Brady can be heard imploring, "Come on David, just knock it in". He was later seen embracing loved ones in tears of joy.

"It was great to see our arrival on such a stage with a team that was actually a good side. It showed people we deserved to be there. I hadn't been there because of what Fifa allowed to go on, or encouraged to go on."

Brady was given a painful reminder of football's cyclical nature, however, in Paris. As he said a few months later:?"The Henry thing was one of the worst incidents in my footballing life. We didn't say it to the players before the game but I always had a feeling... people wanted France there. I think Fifa were paving the way for this to happen. The changing of the draw exposed them totally to what they're all about."

Brady doubts whether anything will ever change. As Charlton showed a generation of players and Brady himself in that hotel though, cycles are there to be broken.

Book Launch

Miguel Delaney's book on the Irish team between 1986-2002, 'Stuttgart to Saipan – The Players' Stories' (Mentor Books) will be on sale in bookshops from this week