Phase two of the Royal Commission of Inquiry into the deaths of 29 men in the Pike River mine concluded this afternoon after days of emotional testimony.

Huge amounts of detail and masses of questions have been brought to light since the inquiry began on July 11.

We highlight some of the main issues raised by families, mines rescue experts, police, Solid Energy and Pike River Coal officials.

1. Was the mine ever safe?

Evidence presented to the inquiry has painted a picture of a mine plagued by cost blowouts, over-optimistic extraction targets, inadequate geological investigation and lax safety standards.

The inquiry heard about a blowout in the Pike River mine construction costs from $29.3 million in 1997 to $207 million in 2007.

Solid Energy chief executive Don Elder said that was accompanied by "over-optimistic" coal extraction targets.

He criticised drilling work at the mine, saying boreholes should have been spaced every 100m rather than every 500m.

Geologist Jane Newman said she told her husband not to go to the Pike River mine because she feared the PRC had not done adequate investigation to operate in the unique geological conditions of the West Coast.

Harry Bell, an experienced West Coast miner who lost his nephew in the Pike River mine, raised concerns about ventilation at the mine.

He once told company bosses a drilling plan was "nonsensical, madness" and told them he would be prepared to be identified as a whistleblower.

2. Was the second exit from the mine adequate?

Major concerns about the lack of a safe second exit out of the Pike River mine have stretched across both phases of the inquiry.

Pike River Coal (PRC) had identified the mine's 108m ventilation shaft, which features a diagonal sloping 'Alimak Rise', as an emergency escape route.

But a 2009 New Zealand Mines Rescue report tabled by counsel for the Pike River dead said it would be "virtually impossible" to climb the shaft if there was a fire in the mine.

Mine safety officer Neville Rockhouse, who lost his son Ben Rockhouse in the disaster, said he never considered the shaft an adequate second egress.

New Zealand Mines Rescue general manager Trevor Watts said he was "gobsmacked" to find the shaft met the minimum standards of the Department of Labour mines inspectorate.

However, PRC chief executive Peter Whittall has maintained the shaft could have been used by trapped miners after an explosion.

3. Who should have headed the rescue and recovery operation?

Mining rescue experts have lamented their lack of input into the command structure set up to respond to the explosions at Pike River.

The structure involved teams at the mine site preparing reports and risk assessments for police in Greymouth.

Those were then filed to police national headquarters and the Department of Labour for approval.

New Zealand Mines Rescue general manager Trevor Watts said the amount of off-site control resulted in "operational paralysis".

He said quick decisions were needed to make sure bodies were recovered from the mine.

Instead one document had to be resubmitted because of a spelling mistake and officials seemed more concerned with issues of liability, he said.

Commissioner Stewart Bell said he was "surprised" that police refused to transfer incident control to one of the "many" local mining experts available.

"How much time was wasted... training police officers... in mining matters when you could have had someone there from the word go that understood the terminology from the word go."

Police and the Department of Labour have acknowledged more decisions could have been made at the Pike River mine site.

However, police assistant commissioner Grant Nicholls said while improvements could be made, the operation was generally run efficiently.

Agencies worked well together and quick decisions were made when they were needed, he said.

4. Did any of the 29 men survive the first explosion?

For five days from November 19, all of New Zealand joined the West Coast community in holding out hope for the 29 men trapped inside the Pike River mine.

Pike River Coal chief executive Peter Whittall told families and media the men may have been clustered around a fresh air line waiting for rescue.

Families of the dead have told the inquiry they clutched onto those words and refused to give up on the chance their loved ones were alive.

However, several organisations have submitted evidence arguing those claims amounted to false hope.

New Zealand Mines Rescue formed the view early on that the force of a 52 second blast inside a small mine would almost definitely have killed the 29 men instantly.

Mr Watts said those that survived the blast would have died from inhaling noxious gasses soon afterwards.

If they had made it to a fresh air base in the mine, their training would have been to don self rescuers and walk out, he said.

Under questioning from counsel for the families, Mr Whittall said the only way men could have survived was to build a brattice shield and cluster around a compressed airline in the upper reaches of the mine.

He admitted it was a slim chance the men had survived, but denied giving families false hope.

Police including assistant commissioner Grant Nicholls and superintendent Gary Knowles said hope for survivors could not have been ruled out before the devastating second explosion in the mine on November 24.

5. Should the mine have been sealed within days of the first explosion?

After concluding the 29 men inside the mine were dead, New Zealand Mines Rescue began asking for the mine to be sealed.

Mr Watts said the sealing option was first presented to police on November 21 and again immediately after the second explosion on November 24.

Their plan was rebuffed by off-site police and the Department of Labour who believed people could still be alive inside the mine.

Sealing the mine earlier would have allowed bodies to be recovered, Mr Watts said.

Important evidence on what caused the explosion could have been gathered and the mine may have been saved for future mining, he said.

The Department of Labour admitted stifling debate on sealing the mine by threatening to issue a prohibition notice stopping the move.

Police assistant commissioner Grant Nicholls said the mine could not have been sealed while there was any chance it could kill a survivor.

One further question remains unanswered:

What caused the explosion?

This question of what caused the first explosion inside Pike River remains a mystery.

Though many of the questions raised so far have alluded to possible reasons for the blast, any direct inquiries have been quickly cut off.

It is set to be the focus of the vital third phase of the inquiry beginning in November.