He questioned their relationship with Unicef and Uefa, running his way through a catalogue of referees, greeting each name – Stark, Ovrebo, Busacca, De Bleeckere, Frisk – with a simple: ¿por qué? He provoked their manager into an astonishing, asterisk-splattered rant and inspired their pointed end-of-season celebrations, watching them sing: "Why? Because we're the best, so fuck you!" He even poked their assistant coach in the eye. Now, José Mourinho could be on the verge of really hurting FC Barcelona.

It wouldn't be the first time, or even the first time Real Madrid's supporters have gloried in his success. But this would be different; this would be theirs. An image presides over Mourinho's office at Valdebebas, Madrid's training complex near Barajas airport. In it Mourinho runs, finger raised, across the Camp Nou pitch after the 2010 Champions League semi-final in which Internazionale knocked Barça out.

Madrid were grateful to be spared watching Barcelona reach a European Cup final staged at the Santiago Bernabéu. That Mourinho would join them was an open secret; Madrid wanted him to do the same for them. Desperation had set in. Florentino Pérez, trophyless in four years as president, saw in Mourinho the only man able to end Barcelona's dominance – a special one to beat a side many called the best in history.

Signing Mourinho represented a revolution. At times, it was a trauma. So much has happened, so much has changed, over the last 18 months – from political battles to moral crusades, for and against – that it can appear impossible to keep track of it all. There's no turning back. Madrid fans do not want to. They're now so close they can almost touch it.Pérez's bet was risky and he was forced to back it heavily, but he may just win in the end.

Last season, Madrid beat Barcelona in the final of the Copa del Rey. It was the least important of three competitions – Barça won a La Liga and Champions League double – but it was a start and it softened memories of a famous, painful 5-0 defeat in La Liga in November. Yet there was criticism too: not just of Mourinho's behaviour – which created a kind of devil/angel dichotomy – but his tactics, which were often seen through the same prism. His approach against Barcelona in La Liga was met as if it was some kind of moral aberration, not just a way of trying to win a game.

Even Alfredo Di Stéfano noted that Barcelona had played like "lions" and Madrid like "mice". Mourinho had demanded an extra striker all year, taking on his own director general in public, but when the Champions League semi-final came, the two he did have didn't start. It was a compliment to Barça but he didn't win. Arguably, there were mistakes: attacking might have been a better bet while the cards that cost Madrid, if questionable, were a product of their coach's approach. And, rather than cowing Barcelona, provocation appeared to motivate them.

Yet Mourinho's conspiratorial discourse provided a justification and the cup was presented as a stepping stone to a challenge on Barcelona. After five successive defeats and a horribly flat draw, winning was possible. Madrid were getting there. The club bought it. Now, it rings true.

Before the Champions League semi-final Pep Guardiola, Barcelona's coach, called Mourinho the "puto amo" – the "fucking master", "the man". Madrid fans, embracing Mourinho like no other coach, agreed. The Madrid media, playing their role, laud him even as they question his behaviour. Now, others agree. Madrid go into El Clásico with six wins in six Champions League matches. They have won their last 15 games by an aggregate score of 57-9. More importantly, they lead Barcelona by three points in La Liga and they have a game in the hand. Win El Clásico and the lead will effectively be nine.

Definitive? Nearly. A nine-point lead in a league where so few points are dropped is colossal. In the last two years Madrid have topped 90 points and not been champions. Barcelona dropped just 14 points last season, Madrid 22. This season Madrid have dropped five in 14 games. Maintain that rate and they will not be overhauled even if Barcelona maintain a perfect record until the final day.

It is not just about the stats – it is also about the sensation. The Madrid-Barça rivalry is symbiotic and cyclical – in the Spanish capital they sense a change, in the Catalan capital they fear one. Madrid are playing well. Very well. Barcelona have won only twice away this season, both by one goal. Madrid are favourites for the first time under Mourinho. Last weekend they beat Sporting Gijón 3-0. Manolo Preciado, the Sporting manager who last season had a public fight with Mourinho and led his side to a 1-0 win at the Bernabéu, called Madrid's form "alarmingly good".

"They are even dangerous when you have possession," he said. "You lose the ball and in two passes they've scored. Their physical condition is stratospheric, their pace bestial. They are like little kids when they lose the ball – desperate to get it back."

The French striker Karim Benzema talked recently of Mourinho turning him into a "warrior".

This summer brought a new mantra: Mourinho's sides are better in the second season. Any coach's side would be, you might think. The difference is that any coach wouldn't get a second season at Real. Mourinho did. He has the authority and the charisma to stay in the job – defeat in the Copa del Rey might have changed that – and no coach has had his name sung at the Bernabéu as Mourinho has; none has accrued power, both populist and political, like him. If the president had sacked Mourinho he would have stood alone. Instead, he backed him.

Arrigo Sacchi once noted that Madrid always undermine coaches' authority, with disastrous effects. One insider says: "Players only see two types of coaches: strong and weak." Mourinho, uniquely in recent history, is the former. This summer, the director general, Jorge Valdano, was sacked on his say-so. The club's model changed: Mourinho, the man the Portugal midfielder Maniche said was "security guard, gardener and coach driver", became manager, controlling everything. The signings were his, the departures too.

Some counselled against the move. In the media there was moral panic. It was, for the critics, a Faustian pact: Madrid had sold their soul to the devil. Mourinho had started countless fires; every press conference was a prelude to war. Where, they said, was the señorío of which Madrid had always boasted, that gentlemanliness? The response was simple: Who cares? We have to win. Pérez publicly, and rather forcedly, redefined señorío to make it fit Mourinho's actions. Madridismo was what Mourinho said it was.

Amid it all, the critics missed an essential truth: Mourinho was right. Madrid's system had to change.

"Madrid needed someone like Mourinho," said the defender Sergio Ramos, "someone with character and personality." Someone who, as one first-teamer says, "empathises with the players, knows when to put an arm round them, but above all is demanding and makes himself respected".

The player-manager relationship has not always been as fluid as the official line would have it, and rarely has a coach been so surrounded by a swirl of propaganda and half-truths. Mourinho's role in recuperating Benzema has been overplayed, as has the warmth with "all" his players. But he demands loyalty and gets it. In his own words, players who break rank "have a cross put on them and to me they're dead". "Respect" is the word.

Respect comes through fear and friendship, but above all through results. "Sometimes he tells you what'll happen and it does – exactly" says Benzema. "I don't know how, but it's incredible."

In the 24 hours before each game, there are two or three tactical talks. Cristiano Ronaldo says Mourinho "studies the opposition like no one" and Kaká talks of "a coach who works hard tactically, likes the team to have great intensity and prepares well with concrete details: how this player moves, set plays, roles". "The work," he says, "is very good indeed."

Mourinho's tactical approach is not revolutionary but the depth of information is striking. Sessions are short but intense, moves repeated to create what Spaniards call automatismos. Rapid transitions from defence to attack and attack to defence are fundamental.

"With the players we have, that's natural," one player says. Kaká says: "We know what to do if we lose the ball – we know we have to return to specific positions and recreate a shape quickly. Attackers have obligations too: we're fundamental in the defensive system. The speed of recuperation is very important."

This summer, there was not one pre-season exercise without a ball. Once, Mourinho prepared a game played with three goals, one at each end and one in the middle. Every player was cramped into the space between the two nearest goals. The defending team had to protect themselves, win the ball and play it over the middle goal into the space beyond, running on to score in the third goal. The aim was to learn through repetition how to reach the space left by teams that pressure high. Teams such as Barcelona.

Classic Mourinho, you might think. But Madrid have evolved too. The sheer speed and precision of their transitions is their greatest weapon – just count the goals scored from opposition corners – and they have scored more and conceded fewer headed goals than anyone, while scoring the most from set plays. "Barcelona will dominate possession but that's the way Madrid like it," said the former Barça midfielder Ronald de Boer. Preciado noted: "Madrid don't need toque [touch] to express themselves like Barcelona." And yet they can do that too: there is greater variety now.

The shift is reflected in Angel Di María. The Argentinian has provided more assists than anyone in La Liga but where once he sprinted into space, dropping the ball off, now it is he who is dropping off and delivering angled passes, Xavi-style. There is more combination to Madrid's game. They average 576 passes per game, compared to 484 last season; their possession has increased from 56.5% to 63.9%. There is less dependence on Ronaldo; less, in fact, than Barcelona appear to have on Lionel Messi.

Madrid have taken a step forward on the pitch: 20 metres forward. Their pressure is more advanced, more intelligently applied and more collective; Mourinho has convinced his players of the need for high intensity and colossal effort. Opponents are being asphyxiated. There are also more shots, and better ones too. Barcelona won the Super Copa season-opener thanks to Messi, but over the two legs Madrid had twice as many shots, with 32. The battle was waged on a more equal footing.

Madrid's players are more comfortable and the media is more enamoured. Ramos has replaced the injured Ricardo Carvalho at centre-back, bringing greater athleticism and recovery and allowing Madrid to advance, but there has also been a natural evolution. One first-teamer says: "You need to be very well-synchronised, quick and organised. That takes time and maybe we weren't ready before. We're comfortable with it now, a better team."

That has brought a different focus: where Mourinho once left attacking to individual inspiration, focusing on defensive mechanisms, there are now pre-planned moves, with specific spaces occupied by specific players.

Mourinho has changed too. Perhaps he feels he no longer needs to play the agent provocateur. Perhaps results have calmed him. Perhaps he has seen that provocation, anger and tension were counterproductive. A 0-0 draw at Santander in September was a turning point. Mourinho's post-match criticism met some resistance in the dressing room. It had often been said that Mourinho starts fires to protect his players, relieving the pressure on them, but they were burnt too.

Some supporters welcomed Mourinho's attacks on Barcelona, seeing a coach who at last refused to turn the other cheek. When Mourinho poked Tito Vilanova in the eye at the start of this season, he didn't apologise and he attacked those who questioned him as "pseudo-Madridistas", presenting himself as the sole guardian of the truth. It convinces some – the commitment to Mourinho's cause from certain players is extraordinary – but not all. Nor, some within the squad felt, was the manager's commitment to players evenly spread. In Santander they told him so. Pérez came to the dressing room to embrace the coach – an unmistakable display of authority.

There was a rapprochement. Mourinho recognised the problem and acted. A barbecue was arranged to project, via official media, an image of unity. Although the digs at Barcelona's "favourable" treatment continue, Mourinho walks a less combative line now, both publicly and privately. Most players have not risked commenting but Ramos did say that talking about referees "has to stop – it does us no good". Mourinho is more relaxed. "I prefer this version, that's for sure," says one player. "A calmer climate helps."

On Friday, the media packed the press room to hear Mourinho speak, hoping for another show. He sent out his No2, Aitor Karanka. There have been no interviews and no fires. There has just been a team preparing for a game that could mark a shift in the power balance in Spain. A manager preparing to do what he came for. Hurt Barcelona. And properly this time.