The trainspotter now arriving in the UAE is the late golden boy

Richard Branson's right-hand man. One of Tony Blair's favourite mandarins. Saviour of Britain's crumbling 3,500 secondary-schools estate. FTSE 100 chief executive. Coveted by Boris Johnson as his deputy mayor.

That's quite a career for someone who is still only 43. And Richard Bowker is this weekend preparing to pack his bags for the United Arab Emirates (UAE), where he will oversee the £20bn construction of a 9,000km railway network.

Despite Bowker's enviable CV, the UAE is a place he was far more likely to find big-time employment than the UK. His reputation has been damaged by a poor tenure at National Express, the trains-to-buses transport giant, where he has been in charge since 2006. Bowker announced his departure last week amid a wave of depressing headlines for National Express shareholders. Rival FirstGroup had a preliminary all-paper approach dismissed, a move which seems to have some shareholder support.

The company's loss-making East Coast mainline franchise is to be renationalised, after National Express admitted it could not make repayments totalling £1.4bn to 2015. Bowker's team has been criticised for walking away at a cost of just £72m, when the public purse will end up taking a hit of hundreds of millions. National Express is also struggling with a £1.2bn debt burden. Not a happy end to Bowker's reign. He will step down as a director at the end of this week and officially leave on 31 August.

Despite the many plaudits Bowker has received throughout his career, there has often been a whiff of controversy about this intelligent, Blackburn Rovers-loving Lancastrian. His rise really began when Branson was on the hunt for the best brain in rail procurement – acquiring and managing contracts. Virgin asked around the City to find out who had done the best job buying trains in recent years and Bowker's name kept coming up.

Before joining infrastructure investor Babcock & Brown, Bowker had worked on the £400m private finance initiative contract providing new trains for London Underground's Northern Line. A source who worked for Virgin when Bowker was on secondment to the company in 1997 says: "That was a very good contract, it didn't go overbudget. He'd built up a very strong reputation and we needed someone to work on procurement of the Pendolino [tilting] trains for the West Coast mainline."

With Branson becoming a big fan of a man who was "always thinking about detail", Bowker joined Virgin Group full-time in 2000, when he was made commercial director. But he was soon headhunted for a grander stage. At just 35, he became the £250,000-a-year chairman of the Strategic Rail Authority (SRA) at the end of 2001. He is said to have rejected the job several times, and maybe he wishes he had stuck to that decision. Arguably, though his star continued to rise, this is where a slightly egotistical manner started to shine through.

"He is very impressed by his own ability," says an industry observer. "The SRA was run like a political party spin machine .... but if you're a regulator you shouldn't spin."

Bowker ran the SRA for nearly three years, extending its hold over the industry, leading rail chiefs to dub it the Stalinist Rail Authority. He quit in 2004, after a White Paper proposed abolishing the SRA. Although his commercial nous helped to attract billions of pounds of investment into the rail industry, he is said not to have got on with Sir David Rowlands, then permanent secretary at the Transport department.

Many passengers were unhappy too, as fares rose above inflation. However, Bowker got on well with the prime minister. A former session pianist, he jammed with Tony Blair.

The next job was the really curious one. The Government wanted to rebuild every secondary school in the country, and had set up Partnerships for Schools (PfS)to oversee the programme. Bowker took over in late 2006, but few believe that he was interested in the job. Within two months, he was interviewed by the Olympic Delivery Authority, while the construction industry regularly speculated that he would soon be off. Despite denials, it was right: after just eight months, Bowker went to National Express.

"Tim Byles [Bowker's successor at PfS] has spent two-and-a-half years clearing up Bowker's mess," says a source. "His style of leadership was 'follow me or fuck off', and the body's relationship with local authorities was shot to pieces."

Behind schedule, Byles reassessed the programme, setting new targets. With more sensible programming, the scheme is ahead of schedule. "It was a really wasted period," says an education sector source. "But I think his heart was always with trains."

There's almost certainly some truth to that: Bowker was a trainspotter as a child. In February this year, Richard Bacon, the Conservative MP for South Norfolk who sits on the Public Accounts Committee, said: "He went from the Strategic Rail Authority when it was wound up to Partnerships for Schools. Which genius had that idea?"

Bacon also commented on Bowker turning up to the committee with no tie and even donning a T-shirt. Such informality is a signature of Bowker, just as it is of his former boss, Branson.

Now a FTSE 100 boss, Bowker would tackle the City as he had government and business. East Coast mainline was his big victory. The contract – employing 3,100 staff and carrying 17 million passengers a year – was secured in 2007.

London Mayor Boris Johnson almost made Bowker one of his deputies; a City source says "they were halfway up the aisle". But, wanting a City heavyweight, Johnson instead chose private-equity baron Tim Parker, who lasted three months. It would have been a good time to have left National Express: the unforeseen financial crisis and recession meant passenger numbers collapsed, wrecking profit estimates on the East Coast mainline.

So once again Bowker leaves a bit of a mess, as well as a job paying nearly £1m a year. The UAE is gambling by putting its plans to link up the seven Emirates into his hands, but his enthusiasm and talent cannot be discounted.

And one man is definitely sad to wave goodbye. Branson is reported to have said of Bowker's move to a warmer climate: "I am sad to see Bowker leave .... He has shown dedication and drive."

Making tracks for the United Arab Emirates

Richard Bowker is heading to the UAE to become chief executive of Union Railway Company, which will oversee a £20bn rail construction programme.

The first phase of the rail network – mainly for industrial use, such as transportation of sand, rock and cement – should be operational in just two years. It should be completed by 2015. The big news, though, is the second phase, which will link up the seven Emirates with a highspeed commuter network. The track will run from the coast to the border with Saudi Arabia.

The government-owned Union Railway Company, which was only formed in March, will also lease, own, buy, sell and operate trains. The UK is developing quite a presence in the UAE’s transport sector. British consultants Mott MacDonald and Steer Davies Gleave were appointed by Abu Dhabi’s transport department to draw up a masterplan for surface transport. Last year, Dubai’s Roads &Transport Authority asked for bids for a rail transit study. British bidders Halcrow, Arup and Hyder onsulting went up against US group Parsons Brinckerhoff.

City fears more government grab-backs

There are fears in the City that the renationalisation of the East Coast mainline could lead to the Government taking back a swathe of major franchises.

Railfuture, the transport campaign group, has even called for an end to the franchise system.

Lord Adonis, the Secretary of State for Transport, is reported to be eager to take away National Express's two remaining franchises. These are National Express East Anglia and c2c.

Already, Lord Adonis has all but warned off National Express from bidding for any upcoming franchises, saying that by handing back the East Coast mainline the group would not meet pre- qualification criteria.

He said last week: "It is simply unacceptable to reap the benefits of contracts when times are good, only to walk away from them when times become more challenging."

Bowker (left) insists that National Express did not make an over-optimistic bid for East Coast by exaggerating its passenger-growth expectations. Bowker said at the time of winning the franchise that National Express did not bid at "unsustainable or undeliverable" levels.

However, Lord Adonis has said that he hopes to offer the East Coast mainline back out to the market next year. His hand might be forced in any case, given that there are concerns that the Government does not have the staff to run rail franchises.