After Scotland Yard scales down its investigation, Gordon Rayner looks at the latest news on the truth about what happened to Madeleine McCann

In the nine years since Madeleine McCann went missing from a holiday apartment in Portugal, myriad theories about what happened to her have taken root, but only one fact remains uncontested: that she was reported missing at 10.14pm on the evening of Thursday, May 3, 2007.  

It was at that point, when police were called, that the clock started ticking on the biggest missing persons investigation for decades, a search which remains very much active to this day.  

Facts, the hard currency of any police investigation, have proved almost uniquely elusive; every sighting, every timing and every witness statement has been disputed in the years that have elapsed since.  

Madeleine’s parents Kate and Gerry McCann quickly came under suspicion by Portuguese police, a development that the couple are certain meant vital clues were missed in the first hours and days after Madeleine’s disappearance.

Every possible theory has been explored since then: that Madeleine was abducted by a paedophile; that she was killed during a bungled burglary and her body dumped; that she was abducted by traffickers and sold to a childless couple; that she wandered out of the apartment and died in a tragic accident, and many more besides.

To date, however, not one shred of proof of what happened to Madeleine has been unearthed. The question of what happened to Madeleine would become not only a personal tragedy for the McCann family, but a national obsession in the UK and in Portugal.

Madeleine, of Rothley, Leicestershire, was on the penultimate day of her family holiday on the day she vanished. She had spent part of the day playing by the swimming pool in the Ocean Club resort, where the last known picture of her was taken at 2.29pm.

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Reports of when she was last seen alive by independent witnesses vary, but she was still alive at around 6pm, when she and her parents went into their apartment at 5A Rua Dr Agostinho da Silva, where Madeleine and her two-year-old twin brother and sister were readied for bed.  

The McCanns told police they put the children to bed at around 7pm, and that all three were asleep by 8.30pm, when they went for dinner at a tapas bar 50 yards across the pool from their apartment. There they met seven friends with whom they were on holiday.

The McCanns say checks were made on their children every half-hour, sometimes by other members of the party, comprising Dr Russell O'Brien and Jane Tanner, from Exeter, Dr Matthew and Rachael Oldfield, from London, and David and Fiona Payne, from Leicester, together with Mrs Payne's mother Dianne Webster. Mrs Webster, however, reportedly told police that each couple was responsible for checking their own children.

Gerry McCann went to the apartment at 9.05pm, when all the children were sleeping soundly and Madeleine was still in her bed, he says.

The police in Portugal, however, have never accepted the McCanns’ evidence as undisputed. They initially regarded the McCanns as suspects, and believed the McCanns could have killed Madeleine any time after the last independent sighting of her at 6pm.

A timeline of that evening shows that Dr Matthew Oldfield went into apartment 5A at 9.30pm, and noticed that Madeleine’s room seemed lighter than the others, as if the shutters had been partially opened. He could not be certain whether Madeleine was there.

Kate McCann was next to check on the children, at 10pm. She ran back to the restaurant moments later, saying Madeleine was missing. The McCanns and their friends made a quick search of the resort, but after finding no sign of Madeleine the police were called at 10.14pm.

The McCanns told police they had put Madeleine to bed with her pink comfort blanket and favourite soft toy, Cuddle Cat, and was wearing short-sleeved Marks & Spencer Eeyore pyjamas.

Crucially, however, the apartment was not initially treated as a crime scene, meaning around 20 people went in and out before it was sealed off, contaminating potential evidence. Roadblocks were not put in place until 10am the next day, border guards were not informed for hours and Interpol did not put out a global missing persons alert for five days.

It meant that the most crucial time of any missing persons investigation – the first 24 hours – were largely squandered, and police have been trying to catch up ever since. Yet potentially key sightings and artists’ impressions of suspects were kept from the public for years.

Mary and Martin Smith, from Ireland, told police they saw a man carrying a child matching Madeleine’s description at around 10pm on Rua da Escola Primaria, 500 yards from the McCanns’ apartment. He was heading towards the beach, did not look like a tourist and did not seem comfortable carrying the child, they said.

Their evidence was compelling, but it was only in October 2013 that two e-fit images of the man, compiled by police from descriptions given by Mr and Mrs Smith, were released by Scotland Yard to coincide with a BBC Crimewatch reconstruction of Madeleine’s disappearance. He remains a suspect.

There were also blind alleys. Jane Tanner, one of the tapas diners, told police that when she left the restaurant at 9.15pm to check on her own daughter, she saw a man carrying a small child, wearing pink pyjamas, in his arms.

For years afterwards, the mystery man would be a key suspect, if not the prime suspect, but in October 2013 the Metropolitan Police announced that a British holidaymaker who had been taking his daughter back to his apartment after picking her up from an evening crèche, had been identified as the man Miss Tanner had seen and ruled out of the inquiry.

The first person to become an “arguido”, or official suspect, was Robert Murat, a local property consultant, whose home was searched 12 days after the disappearance. He was formally cleared of suspicion in 2008 and won £600,000 in libel damages from 11 British newspapers.

The Portuguese Police, however, were suspicious of the McCanns from the beginning, partly due to a clash of cultures. They could not believe that parents would leave their children unattended, and did not approve of the McCanns’ use of the media to raise the profile of the case, in a country where secrecy is the hallmark of all police investigations.

The arrival of two British sniffer dogs in Portugal in July 2007 only hardened that belief. One dog was trained to sniff out traces of human blood, the other was trained to sniff out the scent of dead bodies. Both dogs were taken to several locations connected to the investigation, and gave alerts only in apartment 5A. Later, the cadaver dog gave an alert inside a Renault car, hired by the McCanns 24 days after Madeleine went missing.

DNA tests on samples taken from the car proved inconclusive, but the Portuguese police wrongly told journalists they were a “100 per cent match” for Madeleine.

The Portuguese police came up with the theory that Madeleine had been killed by her parents by accident, possibly by being given an overdose of a sedative to make her sleep, that they had hidden the body, faked her abduction and then used the hire car weeks later to move her body to a burial location.

In early September 2007, according to Kate McCann, she was told by the Portuguese police that if she admitted that Madeleine had died in the apartment and she had hidden her body she might only serve a two-year sentence and Gerry McCann would not be charged at all. On September 7 the couple were both made arguidos.

Goncalo Amaral, the chief inspector who had been in charge of the case, resigned in 2008 to write a book alleging that Madeleine had died in an accident in the apartment and the McCanns had faked the abduction. The McCanns sued him for libel, with the court expected to make its decision in 2015.

In July 2008 the Portuguese attorney general announced that the McCanns were no longer suspects and the investigation was closed. The McCanns hired private investigators to carry on the search, but it was not until May 2011 that Theresa May, the Home Secretary, announced that Scotland Yard would review the evidence in the case, which had until then been the responsibility of Leicestershire Police, working with the Portuguese authorities.

In July 2013 Operation Grange, the review of the available evidence, became a full-blown criminal inquiry, and Scotland Yard said it was concentrating on a “criminal act by a stranger”.

The Yard announced it was looking into possible links between Madeleine’s disappearance and bogus charity collectors who were knocking on doors in Praia da Luz at the time. Between 3.30pm and 5.30pm on the day in question there were four separate sightings of men who said they were collecting money for an orphanage. British detectives believe men whose photofits they released in 2013 may have been engaged in reconnaissance for a pre-planned abduction or for burglaries, in keeping with the theory that Madeleine may have been killed by a burglar she disturbed.

Scotland Yard also said in 2013 it was eager to trace a blond-haired man who had been seen loitering in the area on April 30 and May 2, looking at apartment 1A. He was described as “ugly” with a spotty complexion and a large nose. Two blond-haired men were seen on the balcony of the empty apartment 5C, two doors from 5A, at 2.30pm on the day of the disappearance. Blond men were seen again near 5A at 4pm and 6pm that day, and at 11pm that night. Following the appeal on Crimewatch, the Portuguese police re-opened their own investigation.

Scotland Yard officers travelled to Portugal in 2014 to interview four suspects and carried out searches of the area around the apartment using ground-penetrating radar. One of the men who was interview has since been eliminated from the inquiry, but the other three men remain arguidos.

The British officers questioned them on suspicion of being part of a burglary gang that panicked after killing Madeleine during a bungled break-in. They all protested their innocence and were released without charge.

Another suspect was Euclides Monteiro, a convicted burglar with a drug habit, who had been sacked from the Ocean Club in 2006. Mobile phone tracking showed he had been in the area on the night of the disappearance, and police believe he may have been burgling apartments there to fund his drug addiction. He died in a tractor accident in 2009.

In March 2014 Scotland Yard announced that a lone intruder sexually assaulted five girls aged between seven and 10 in the Algarve between 2004 and 2006. The man, who has never been caught, was said to have a “very, very unhealthy interest” in young white girls.

The four incidents, one of which involved two girls, were among 12 in which men had entered holiday accommodation in the area, including two incidents in Praia da Luz. The force also said it was looking at 38 “people of interest” and were researching the backgrounds of 530 known sex offenders, including 59 regarded as high interest.

In December 2014 Det Chief Insp Andy Redwood, the man who had led Operation Grange, retired and was replaced on Dec 22 by DCI Nicola Wall, who travelled to Portugal the same month to conduct further inquiries.

DCI Wall and her team interviewed seven suspects and four witnesses, but have not released any information about what they discovered, insisting they will not provide a "running commentary" on the case.

In September 2015 the Met announced that it was scaling back the Operation Grange investigation team from 29 officers to four. With the cost of the inquiry topping £10 million, the force said it was following "a small number of focused lines of inquiry".

It added that the "vast majority" of the work of Operation Grange had been completed. In total officers had reviewed more than 40,000 documents, took 1,338 statements and collected 1,027 exhibits.

The Met said 60 "persons of interest" had been investigated, 650 sex offenders considered and 8,685 potential sightings investigated.

Kate and Gerry McCann remain convinced their daughter is alive and that they will one day be reunited. The hunt to find her continues.