The attack on the US consulate in Benghazi was striking for a number of reasons: the date, 11 September, the toll – four diplomats killed, including an ambassador – and the knock-on effects on the careers of senior American politicians.

But what is perhaps most striking is the inconsistencies: the US version of events compared with those of witnesses and the facts on the ground. The two do not tally. And so, a year later, there remain pressing questions about what happened that night – and what the Americans say happened.

6:43am

Event Staff at the US special mission in Benghazi woke on 11 September to the sight of a Libyan policeman, deployed to guard them, filming the compound from a neighbouring rooftop. When challenged, he vanished. Later, an unmarked car made lazy circles around the compound, a walled redoubt rented in the southern suburbs of the Libyan city.

US version The state department says there were no warning of impending attack, a spokesman insisting there was "nothing unusual during the day at all".

Conflicting evidence Two days earlier, the ambassador to Libya, Chris Stevens, had received a veiled warning. According to one of his cables, one of his diplomats had a meeting with two Islamist militia leaders in which they complained that the US was supporting a secular leader, Mahmoud Jibril, in a vote for prime minister due on 12 September. If Jibril won, they warned, they would "no longer guarantee security". The consulate was already relying on one of the militias, the February 17th Martyrs Brigade, for armed protection.

In the words of a subsequent report by the US Senate's homeland security committee, warning lights were "flashing red". As the day went on, news came in of attacks by radicals on the US embassy in Cairo, a response to a film, the Innocence of Muslims, released in America which mocked Muhammad. The CIA sent a cable to its foreign stations warning of possible copycat incidents.

The anniversary of the 9/11 attacks also preyed on the minds of compound staff in Benghazi. In a letter found in the ruins by the Guardian, Stevens wrote: "For security reasons, we'll need to be careful about limiting moves off compound and scheduling as many meetings as possible in the villa."

At least one man inside the compound was anxious. Sean Smith, a 34-year-old information management officer accompanying the ambassador on the visit, emailed a friend: "Assuming we don't die tonight. We saw one of our 'police' that guard the compound taking pictures." Hours later, he was dead.

9:30pm

Events Diners at the Venezia, an upmarket restaurant across the street from the mission, watch as a dozen armed militiamen gathered in the dusk by the compound's rear gate. The compound comprises four buildings spaced among gardens and surrounded by a breezeblock wall.

One of the militia jeeps bore the black banner of a local Islamist militia, Ansar al-Sharia. The militiamen made no attempt to hide. Men sipping coffee on the pavement outside a nearby cafe saw two pickup trucks packed with militiamen bearing the same banner heading for the mission. Neighbours saw militia 4X4s blocking streets leading to the compound. All were surprised there was no reaction from the compound.

"There were eight to twelve guys, just hanging around, by the gate," one diner said. "They had guns, they were just waiting. There was one Ansar Al Sharia flag. About ten minutes later there were these booms from over the other side (of the compound). The gate came open and this guy put his head out and they shouted at him, get back inside."

US version The state department insists the compound had been well fortified in the spring. The walls had been raised to 3.6 metres (12ft) and topped with barbed wire and concertina barbed wire. The villa had been prepared as a redoubt in the event the walls were breached. It was surrounded by sandbagged emplacements and fitted with grilles on the windows and bulletproof steel doors. Security cameras covered the site.

Conflicting evidence Most of the wall running around the compound had not been heightened beyond around 8ft. The rear wall also had no wire. Two days after the attack the landlord showed the Guardian where attackers had scrambled over. "It was easy for them," he said. Whether cameras were mounted outside the compound is unclear. But failure to see what diners at the Venezia could see in the 10 minutes before the attack would have catastrophic consequences.

9.42pm

Events The diners heard muffled explosions from the far side of the compound. The militiamen outside readied their weapons. Then the metal gate swung open and an unarmed Libyan guard put his head out. One of the militiamen ordered him back inside. The guard pulled the door closed. After a few moments, the militiamen opened fire. "At that moment everyone ran to the back of the restaurant," said one diner.

The first thing occupants of the compound knew about the forces massing against them was the sound of shouting and detonations at the front entrance. Gunmen got in by walking up to a small cabin by the front gate, jamming a gun in the face of an unarmed Libyan guard and demanding he open up.

On the monitor at the communications hub known as the tactical operations centre (TOC), an agent from diplomatic security service (DSS), the state department's security force, saw the front gate open, armed men streaming through, and Libyan guards running for their lives. He activated the alarm.

US version The state department insists security was more than adequate that night, because five DSS agents were in place, more than the recommended three, supported by five unarmed Libyan guards and three armed militiamen from the February 17 brigade.

Conflicting evidence In the preceding months Stevens had cabled three times (7 June, 9 July, and 15 August) asking for more protection or that plans to draw down security be halted, according to the House oversight report. Those months had seen escalating attacks against foreign targets in the city. Commonwealth war graves had been smashed, the Tunisian consulate stormed, a Sudanese diplomat attacked, a UN convoy bombed and the office of the International Committee of the Red Cross rocketed. After two bodyguards of British ambassador Dominic Asquith were wounded in a rocket attack on the UK consulate, London closed its mission down. The US mission had been struck twice by home made bombs thrown at the outside wall.

But even as attacks in Benghazi escalated, Washington decreased security, in line with its official position that Libya, post revolution, was normalising. Three quick-reaction DSS units, named situation security teams, deployed in Tripoli, were withdrawn in the summer, despite objections from their chief, Colonel Andrew Wood. He later told CBS that losing those units was like "being asked to play the piano with two fingers".

On 15 August, the day after Wood was withdrawn, Stevens cabled Washington to say that security in Benghazi was left dangerously exposed. He worried that February 17 was becoming unreliable: a dispute over payment by the embassy meant the brigade's militiamen no longer guarded convoys outside the compound. In addition, the police officers supposed to guard the mission were often late. "Many hours pass when we have no police support at all", he wrote.

The Pentagon's regional headquarters, Africa Command, based in Stuttgart, Germany, offered to send soldiers to fill the gap, but Stevens declined, according to an official review of the incident (pdf). The result was that on the night of 11 September dozens of attackers were surging through the main gates, ranged against a force of five DSS agents.

There are questions over the readiness of this small security detail. Four of the agents were with Stevens as the attack happened, while the fifth was in the TOC. In the event the outside wall was breached, the procedure was to take position at the sandbagged emplacements. But three of the four agents with Stevens had left their rifles, helmets and body armour in the accommodation block, according to the official review by the accountability review board, ordered by former secretary of state Hillary Clinton. Standard procedure for the US army in hostile deployment is for weapons to be carried at all times, even on trips to the bathroom. Why the DSS agents did not have a similar rule is unclear.

They sprinted across the compound to the accommodation block to get their weapons while the remaining agent, who had his rifle, hustled Stevens and Smith inside. By the time the other three had their weapons, attackers were around the villa blocking their path. They retreated, locking themselves into safe rooms in the barracks and TOC, along with the agent already there. With only one DSS agent at the villa, the plan for all-round defence was no longer possible.

9.50pm

Events Inside the villa, Stevens sent a frantic message to Gregory Hicks, America's deputy ambassador in Tripoli, telling him: "We're under attack," according to Hicks's testimony to a House of Representatives committee. The chief of Benghazi's supreme security committee, Libya's gendarmerie, Fawzi Yunis Gaddafi, no relation to the former dictator, was phoned by frantic diplomats. "I spoke to the Americans, they were saying 'please help us'," he told the Guardian.

Inside the compound, the attackers set fire to the guard house near the gate and others rushed to the villa. A rocket-propelled grenade slammed into the lintel above the front doors, jarring them open, and gunmen rushed inside. The lone DSS agent led Stevens and Smith into a final place of refuge, the "safe haven", and locked the gate. Gunmen, unable to penetrate the refuge, dragged furniture outside and threw it into the pool. Others wrecked the villa interior, poured fuel on the floor and set it alight.

US version The safe haven was a walled-off section of the villa constructed with sturdy doors to provide a final refuge in the event the villa was stormed.

Conflicting evidence The safe haven, constructed in the spring, had a serious flaw. The door to the haven was not solid metal, but a gate of thick steel bars, secured by two locks. Its obvious disadvantage was that it offered no protection against smoke should the villa be set on fire.

10:15pm

Events In minutes the villa was blazing fiercely, filling the safe haven with smoke. The DSS agent led Stevens and Smith to an escape hatch in the wall. He tumbled out to the patio outside, only to find the diplomats had not followed. He returned to hunt for them, but was forced back by the smoke. Finally, gasping for breath, he clambered up a ladder to the roof where he phoned his DSS comrades.

The other DSS agents, meanwhile, were locked in the two safe rooms built in the TOC and barracks. The attackers entered the buildings, ransacked each and set them on fire, but did not penetrate the safe rooms.

On the roof of the villa, the agent, his voice hoarse from smoke inhalation, phoned his comrades and told them the situation. The four agents broke out of their safe rooms and met him. Nearby was a white armoured 4X4 which the attackers had not wrecked. The location of the attackers was not clear. The agents were able to get into the vehicle, start the engine and drive the short distance across the compound to the blazing villa. Here, they too went into the safe haven to look for the diplomats, but were driven back by the smoke.

US version State department accounts say the agents were under prolonged fire throughout their ordeal, with battle raging in the compound grounds. "There is considerable firing going on outside," one spokesman briefed journalists. "There are tracer bullets. There is smoke … there are explosions. I can't tell you that they were RPGs, but I think they were RPGs. So there's a lot of action going on."

Conflicting evidence The testimony of heavy fighting is hard to reconcile with the lack of bullet holes in the buildings. The villa's sandy walls are still blackened by the smoke from the fire, but there are few bullet marks here or on the other buildings, nor are there spent casings visible, at least on the paths and asphalt. The front gate has no sign of damage except two bullet holes. The only sign of heavy firing is at the rear gate, with holes from 23 rounds fired into the compound and six fired out. This gunfight is not mentioned in accounts made public. From the time of the attack to the time they were summoned, four of the five DSS agents were in hiding.

10.25pm

Events A six-strong force of Americans with 40 friendly militiamen fought their way through to the compound from a second US base a mile away. At 10.50pm the message "firing has stopped" was sent to Washington.

At the villa, they met the five DSS agents, suffering from smoke inhalation, and got into the safe haven through the escape hatch. They found the body of Smith and dragged it out. Stevens was still missing. The compound was now clear of attackers and the reinforcements took charge, ordering the five DSS agents to leave. Outside the compound their 4X4 was ambushed, bullets slamming into the bodywork and shredding two tyres, but they made it to the second compound. The new force spent 15 minutes hunting for Stevens before deciding they were too few of them in the event of a new attack. At 11pm they abandoned the site with Stevens still inside the villa.

US version The most authoritative of half a dozen investigations initiated in Washington is the accountability review board report, mandated by law. According to the report, compiled by senior intelligence and state department officials, the relief force are "US personnel" and their base an "annexe" to the mission. Charlene Lamb, the state department official responsible for embassy security, testified that the reinforcements were a "quick-reaction team stationed nearby". The Senate's homeland security report described the second base as a place "used by another agency of the United States government". America's UN ambassador, Susan Rice, said the second base was "its annexe".

Conflicting evidence The second base was not an annexe, but a CIA facility, according to Frank Wolf, a US congressman who represents the district that contains CIA headquarters in Langley, Virginia.. It operated independently from the consulate, and its staff of between 22 and 26 agents dwarfed that of the consulate, and its normal complement of two diplomats.

It was these agents who formed the force that battled into the compound and took charge. Yet the term "CIA" did not appear once in the otherwise minutely detailed unclassified version of the accountability review board report.

The apparent desire to shield the CIA from scrutiny in Washington reached farcical proportions last November when Lamb testified to the House of Representatives' oversight committee.

She produced a blow-up photograph of the CIA facility, but before she could explain what it was, panel member Jason Chaffetz, a Republican congressman from Utah, called for it to be removed. The committee chair, Darrell Issa, another Republican, was at first incredulous: "These are people from the state department … I assume they wouldn't come here unless it's cleared."

Chaffetz stuck to his guns: "Mr Chairman, I was told specifically while I was in Libya I could not and should not talk ever about what you are showing here today."

Lamb's team confirmed the photograph was not classified and was available on Google Earth. After a short discussion, Issa ordered it removed: "We're not going to point out details of what may still in fact be a facility of the United States government."

In fact, by the time Issa spoke, the compound in Benghazi was no longer a US facility. The two landlords who owned it showed the site to the Guardian two days after the attack, pointing to the Libyan families they were already moving into the accommodation vacated by the Americans. Signs of the US tenants were still visible: blood covered one wall, a whiteboard by the gate bore the instruction "Take out your trash" and the American's equipment in black packs was stacked on a wall awaiting collection. And the place had never been secret, at least not from Benghazi residents. The landlords insisted neighbours in the tree-lined residential street knew Americans lived there and that their vehicles were a familiar sight.

The bigger question, so far unanswered, is what the CIA was doing in Benghazi. Neither the accountancy review board, the state department nor half a dozen congressional committees investigating the death of Stevens have made any public comment on the role of the CIA; nor have congressional committees tasked with performing the role of scrutinising the government on behalf of the electorate.

00.00 12 September

Events Shortly after the CIA and DSS units arrived at the CIA base, it came under rocket attack. The occupants braced themselves for an assault. Meanwhile, seven embassy and CIA staff in Tripoli chartered a plane and flew to Benghazi, to be met by February 17 militia who escorted them across town to the CIA base. They arrived at 5am. Minutes later, it came under mortar attack. The first bomb fell beyond the walls, but the attackers then "walked" the shells into the compound. Two shells exploded on the roof, killing two CIA security contractors, Glen Doherty and Tyrone Woods. A third man was wounded.

At dawn, reinforcements from February 17 and the Libyan police arrived at the base. They escorted the Americans to the airport for evacuation to Tripoli.

US version Evidence given to the accountability review board described an assault against the base with heavy small arms fire.

Conflicting evidence The lack of bullet marks on the walls of the facility does not square with reports that it was assaulted. Rockets were fired at one wall, and mortar bombs struck the roof, suggesting the firing was opportunistic and from a distance, rather than an attempt to overrun the CIA compound.

00.15

Events When the CIA team abandoned the consulate, crowds of local men and boys gathered at the edge of the fighting moved inside. The fires had died down and they gingerly explored, finding the unsecured window into the safe room. Inside they found Stevens, lying in shirtsleeves on the floor. A video, timed at quarter-past midnight, shows them carrying the ambassador outside on to the patio. When he shows signs of life there are cries of Allahu Akbar – God is Great – and bystanders discuss getting him to hospital.

US version Washington maintains that every possible effort was made to locate Stevens in the hours after the attack.

Conflicting evidence Bystanders put Stevens into a private car. A wounded Libyan guard who left his bloody handprint by the front gate was located and put into a second car. The two cars raced to the city's main casualty hospital, Benghazi Medical Centre. Its director, Dr Fathi al-Jerami, said staff were astonished when the two casualties arrived at the emergency ramp, with the Libyan guard insisting his companion was the ambassador. Medics could not imagine the ambassador would be left unguarded, nor that, if he was missing, no official would try to contact the hospital. He was rushed inside and doctors fought for 90 minutes to revive him before declaring him dead.

Still with no communication from US officials, a hospital official found a mobile phone in Stevens pocket and began punching out dialled numbers. One of these was the phone of an agent now in the CIA base, but the official's English was too rudimentary.

Only in the morning, with US officials being evacuated to the airport, did Americans go to the hospital, to be given Stevens' body. Pictures of the dead ambassador uploaded by Libyans spread across the internet.

16 September

Events On the Sunday following the attack, Susan Rice, America's ambassador to the UN, gave interviews to TV networks ABC, CBS, NBC, CNN and Fox News to offer an explanation for the attacks on Benghazi.

US version Rice said she believed the attack was the result of a protest against the Innocence of Muslims film which had escalated: "The currently available information suggests that the demonstrations in Benghazi were spontaneously inspired by the protests at the US embassy in Cairo and evolved into a direct assault against the US diplomatic post in Benghazi and subsequently its annexe," she said. "There are indications that extremists participated in the violent demonstrations."

Conflicting evidence Within hours, her claim was being disputed in Libya. Mohammed Magaraif, Speaker of the Libyan Congress, was visiting Benghazi to meet survivors and blamed elements of Ansar al-Sharia's militia for the attack. His comments matched those of witnesses.

In America many were surprised Rice was chosen to make a statement about the death of the first US ambassador to be killed since 1979. More properly, the announcement belonged to Hillary Clinton, or possibly the president himself. There was speculation that Rice, the president's foreign policy adviser during his 2008 election campaign, was being given a high profile in readiness for her to step into Clinton's shoes if Obama won a second term in the November election.

Evidence from the US survivors, debriefed on American soil, confirmed the Libyan version of events. There was no protest. Unlike much of the Muslim world, Libya saw no protests against the release of Innocence of Muslims. Ten days after the consulate was stormed, thousands of Benghazi residents, some carrying American flags and placards mourning Stevens, stormed the base of Sharia, setting it ablaze.

Arguments broke out over who gave Rice the information leading her to declare the attack the result of a protest. It morphed into fierce arguments over Obama's competence in the runup to the election. After his re-election, Obama named Rice as secretary of state. Republicans in Congress blocked the nomination, saying they no longer trusted Rice as a result of her Benghazi remarks.

2012-present

Events The FBI opened an inquiry into the Benghazi killings in September. In August 2013 the justice department announced an undisclosed number of indictments against unnamed suspects. Leaks from the Obama administration named Sharia's commander, Ahmed Abu Khattala, as among the suspects. Khattala gave media interviews in Benghazi saying he was at the scene of the attack, but insisting he had come to offer help.

Two Tunisian suspects were arrested in Turkey, and an Egyptian was shot dead in an arrest operation by Cairo police. Libya announced it had made several arrests, but no one was brought to trial. The father of one of those arrested told the Guardian those held were charged, like his son, with looting.

US version On 9 August 2013, Obama said the investigation into the attacks remained "top priority". He added: "We're going to stay on it until we get them." Issa promised that he and his House committee would continue its scrutiny until it got to the truth: "It is our job to work tirelessly in partnership with citizens watchdogs to deliver the facts to the American people."

Conflicting evidence It took four weeks for the FBI to travel to the Benghazi consulate site. By that time the area had been combed over by journalists and the curious, contaminating the evidence. Even after the FBI visit, it was possible for the Guardian to recover classified documents scattered there. In Tripoli, diplomats contrasted the slowness of the FBI with French forensic specialists who were on the ground the day after France's embassy in Tripoli was bombed in April.

Congressional committees continue to grind through the evidence and excise all mention of the CIA.

One year after the killings, no suspects have appeared in court, either in Libya or in the US. Until that happens, and until the gap between claims made in the US and reality on the ground is explained, the American public will remain in the dark about the events of 11 September 2012 in Benghazi.