Just minutes after cafe worker Elly Chen’s trembling hands held up a black flag with white Islamic writing in the window of the Lindt Café, the NSW counterterrorism squad was putting its well-rehearsed strategies into action.

Police officers were on the scene within minutes of receiving a call from a member of the public. She was convinced she had seen a shotgun in the blue sports bag the bandanna wearing man had carried into the popular up-market cafe.

As the sliding glass doors were disabled, officers with guns drawn were already sidling up to the corners of the cafe while others began to evacuate buildings in the area.

Police Commissioner Andrew Scipione said the people trapped inside were “very brave people who in many cases were just buying a cup of coffee and they got caught up in this dreadful affair.”

The Police Executive, Commissioner Scipione, Deputy Police Commissioner and his three deputies Catherine Burn, Dave Hudson and acting deputy Jeff Loy were briefed in a secure room on the 14th floor of Police HQ on the phone by the head of the counter terrorism, Assistant Commissioner Mark Murdoch.

NSW police commissioner Andrew Scipione in Martin Place. Picture: John Grainger Source: News Corp Australia

It took less an hour after the gunman entered the cafe to declare the situation an act of potential terrorism and to deploy the entire resources of the 500 strong counter terrorism unit.

Meanwhile in Canberra, Prime Minister Tony Abbott convened a National Security meeting of cabinet for a briefing on the situation.

Inside the cafe the gunman was forcing the hostages to stand with their hands up against the windows in what was the start of a two hour rotating shift of human shields.

Police protocols developed for years for such a situation were immediately rolling into place.

The operation began was split in two — Strike force Pioneer began to take control of the situation with the deployment of snipers, heavily armed members of the Tactical response Unit, the bomb Squad and highly trained negotiators.

Meanwhile, Strike force Eagle set about investigating who may have been behind the siege. Detectives began gathering intelligence on any possible suspects including known extremists or those associated with extremist groups.

Armed police officers point as they stand at the ready in Martin Place / Picture: AP Source: AP

Operatives began calling community members and other intelligence sources and within two hours they had identified the gunman as fake sheik Man Haron Monis, a 50-year-old on bail as an accessory for the murder of his ex-wife.

His lawyer was contacted and asked to come and help police find a key to getting Monis to give himself up. The FBI passed on information that Monis was on its watch list.

At that stage it was known Monis had a shotgun but officers were concerned that he was wearing a backpack which could contain a bomb that could be detonated if he was agitated, spooked or shot.

Police snipers were watching his every move from the Channel Seven building opposite the cafe.

Twice in the afternoon hostages broke free from the cafe. They were able to give police vital information on the gunman’s state of mind and the hostages left behind.

It also prompted gunman Monis to warn that the next hostage to escape would be met with an eye for an eye and a hostage would be shot. He also became increasingly frustrated that his message was not getting out.

Police Bomb Squad officers at the scene / Picture: Bill Hearne Source: News Corp Australia

He forced hostages to go on social media, make videos and call media organisations with his demands for an ISIS flag and an interview with the Prime Minister.

As night fell and those inside the cafe were fed, it became a war of attrition. Inside the cafe he turned the lights out in a futile attempt to thwart the police’s sophisticated monitoring equipment.

“The police would have been prepared to sit it out for days if necessary,’’ said a counter terrorism expert.

But the plan changed dramatically at just after 2am. Monis started to fall asleep and the hostages decided to make a run for it.

Police Commissioner Andrew Scipione said: “Gunshots were heard ... then (police) moved to an emergency action plan.

“They believed that if at that time (police) didn’t move then there would be many more lives lost.”

Police officers on the ground relayed instantly that the hostages had made a break for it and a shot had been fired. A sniper reported that a hostage was down.

That combination of triggers prompted assistant commissioner Mark Jenkins, who was in charge of the operation at the time to give the order to engage in the assault.

“Going in the way they did is the last resort and only would happen when certain triggers are activated. Gunshots is obviously one, hostages running from the building is another,’’ said the counter terrorism expert.