Designing a fitting tribute to those who died in the attacks on 11 September, 2001 has been a long and complex task

This proud father will join the throng at the site of the World Trade Centre, greet old friends, pay his respects to the thousands who were killed, then shed a few tears as he takes a quiet moment in private reflection.

It’s a routine that has become as familiar to him as writing to his son John, who was killed when the North Tower collapsed, on every birthday, Christmas, Thanksgiving and Father’s Day. This year, however, something will be different. For the first time since the Twin Towers fell, those who gather to honour the dead will not be doing so in the middle of a giant building site.

Instead, the ceremonies will take place at the official 9/11 Memorial, which will open on 11 September and allow the families of those lost to remember their loved ones amid more than 400 trees and two huge reflecting pools with cascading fountains where the towers once stood.

The names of each of the 2,983 victims of the 11 September, 2001 attacks in New York, at The Pentagon and in Pennsylvania, and of a 1993 bombing of the Trade Centre, are inscribed in bronze panels surrounding the pools.

And in a victory for police and fire chiefs who wanted the heroism of their fallen comrades to be recognised, the names of the first responders who lost their lives when the towers fell will be listed together.

“It’s important to have it that way,” says Napolitano, a retired police officer who spent days in the aftermath of attacks sifting through wreckage for survivors and desperately searching for his son, a 33-year-old lieutenant with the New York Fire Department’s Rescue 2 Company.

“The city didn’t want to dwell on that too much, they didn’t want what they saw as a hierarchy of death. But I’m a Brooklyn boy. If your kid got killed trying to save my kid, every day my knee hits the ground to pray for your kid, because I’m praying for yours.”

A subterranean museum on the site, planned to be completed next year, will include as an exhibit a fire engine retrieved from the wreckage, which Napolitano is sure he and his friend Lenny Crisci searched amid the chaos and confusion of the hours after the attack.

“It’s symbolic that [the museum] will be quiet so you can reflect and take in what you see,” he says. “Above ground, it’s New York, there’s always somebody selling police and fire department hats, hotdogs and pretzels, and so on. That’s not the right climate.”

The beauty of the eight-acre memorial and the tranquillity of the museum belie the bickering, political infighting and construction delays that have dogged the reconstruction of the 16-acre site.

Even before the last of the 1.8 million tonnes of rubble were removed from Ground Zero to landfill at Staten Island’s Fresh Kills, the victims’ families complained that they were being cut out of the consultation process for the memorial.

There was tension between Michael Arad, the winner from more than 5,200 entries of a competition to design it, and Daniel Libeskind, the architect with overall responsibility for the entire site, over certain components.

And New York mayor Michael Bloomberg, along with officials from the Lower Manhattan Development Corporation, the Port Authority of New York and New Jersey, the WTC Memorial Foundation and groups representing victims and survivors all wanted a say.

Shortly before the fifth anniversary of the attacks, in 2006, and with costs soaring to more than $1 billion (£536 million), the project came close to collapse. A series of compromises and redesigns put things back on track, but even at the ground-breaking in August 2006, Memorial Foundation president Joe Daniels was requesting public donations to cover a shortfall of more than $200m on the revised $700m budget.

“It was always clear that there were too many people and organisations with conflicting interests involved in the World Trade Centre site for anything there to go smoothly,” says Ted Loos, a New York Times writer who has followed the wrangling from the outset.

The memorial will open on Sunday, two years behind schedule. The rest of the site, originally planned to feature five new skyscrapers, has also suffered serious setbacks and delays, and although ground has finally been broken on four of them, the final look is uncertain. It will be 2013 at the earliest before the first tenants can move in.

The 105-storey building known as 1WTC will be the site’s showpiece and, at 1,776ft tall – commemorating the year of American independence – will become the tallest in the country. Redesigned three times, it generated controversy for a lack of office space and for its “dull” aesthetic, according to some critics.

Towers two and four, along Greenwich Street, will rise to 1,349 feet and 977 feet respectively. Construction on both began only three years ago and 2WTC will not be complete until 2015.

The buildings will eventually appear as bookends to the 80-storey tower three, construction of which, developer Larry Silverstein announced in July, could be further delayed by a lack of private funding.

Meanwhile, plans to construct a 42-floor tower five on Liberty Street, at the south end of the site, have fallen through, largely because of the recession. A proposed performing arts centre has been relocated to tower two.

Despite the problems, politicians say the finished site will be an enormous asset to the city.

“The ongoing redevelopment of my Lower Manhattan community and the progress we continue to make are important symbols to the world of the resiliency of our city and that the victims of the heinous acts of September 11, 2001 will never be forgotten,” said Sheldon Silver, speaker of the New York Assembly.

For survivors such as Patty Clark, a Port Authority employee who descended more than 60 flights to safety in the North Tower shortly before it collapsed, the rebuilt WTC will leave lower Manhattan more vibrant than ever.

“It’s wonderful to see what’s happening there, even in a decade how the whole area has blossomed, the rebound has been astonishing,” she says. “This is going to be the crowning piece, it’s going to be even better than ten years ago.”

Clark still works as a senior aviation adviser for the Port Authority, the site’s owners, so has a closer interest than most. But she still finds it difficult to talk about her memories of emerging into daylight, covered in ash, after a traumatic scramble for survival through dark and dangerous stairwells and the wreckage of the recently fallen South Tower.

“I have very vivid images,” she says. “We were all altered that day. The memorial is fabulous, done really brilliantly to symbolise a lot of things, those who gave the ultimate sacrifice, the victims of attempted murder, those who sat by TVs … things were never quite the same. We’ve picked up and moved on but it’s still there.”

Clark won’t be at the memorial service, preferring instead to be at her son’s soccer game. “Because just like September 11, 2001, my goal is to get back to my son, who was 15 months old at the time,” she says. “It’s my job.”

Napolitano says he has found it difficult to move on, feeling anger that granddaughters Elizabeth and Emma, now active young teenagers, have grown up without their father.

“A million, trillion Bin Ladens wouldn’t equal my son, or any of the other heroes who died that day, or any of the victims,” he says. “At the time, my daughter-in-law Ann spoke to them and let them know they only had their Daddy for a short time, but they had the very best Daddy. They understand, they know who their father was.”

The girls will accompany their grandfather to the World Trade Centre for only the second time, with other family members and several close friends there for support.

At the fifth anniversary, Elizabeth and Emma, then 11 and eight, “watched like they were looking at a movie” as Napolitano showed them Ground Zero and where their father, and Lenny’s brother John Crisci, died.

“They didn’t ask too many questions but as we were walking away they turned around, maybe looking to get one last glimpse of their dad,” he says. “My son’s not a hero because he died saving lives, he’s a hero because he lived saving people.

“Time is a relentless enemy. What happened ten years ago lives with me every day, I carry it with me always. I breathe the ash, I smell the smell of that day. It haunts me.”