So how was the puzzle cracked?
The Business Herald got the inside story from legal adviser and backroom Fonterra innovator Pat Bowler.
He is a self-effacing man and does not seek the limelight.
The chairman of the large Russell McVeagh law firm quit litigation in preference for the anonymity of a commercial lawyer. But he was a driving force behind the Fonterra deal, extending his role as lawyer to become mediator, counsellor and deal-maker.
He was the middleman who held the hands of both the Kiwi Dairies and NZ Dairy Group boards, then slipped out of the loop when they were finally enamoured of each other. He was the one who wooed the Government into closing the Commerce Commission's eyes to New Zealand's biggest commercial deal.
Mr Bowler has a history of closing big deals and Fonterra, surely, was a highlight.
"I don't want to sound egotistical," he said, "but the jobs I get involved with at this stage in my career are very absorbing."
The honour came from being asked to do it in the first place. Mr Bowler had done Dairy Board tasks since 1996, but this had a different ring about it.
The collapse of the 1999 merger attempt was fresh in Dairy Board executives' minds when they contacted Mr Bowler.
"I was asked to do a peer review of the competition work that was done on the project, and the question for me was whether they were putting together an appropriate application to the Commerce Commission.
"My advice was that they wouldn't succeed and they were going about it the wrong way."
He was asked to steer another merger attempt and was put in the unusual position of advising both parties - Kiwi and Dairy Group - as one client.
"Yes, it sounds a bit scary, doesn't it, like their interests weren't being looked after? But in fact what they were trying to do was find some common ground," Mr Bowler said.
"I can't emphasis it enough; this was a single team. The two companies agreed they would not use independent lawyers. It was very unusual for a commercial deal.
"I used to go along to meetings where they'd be shouting at each other, and they'd say to me, 'What do you think?' rather than what does the Dairy [Group] lawyer think, and what does the Kiwi lawyer think. It was project-orientated, rather than specific client-orientated."
There was the time he had to run between the rooms of a South Auckland hotel, pacifying and speaking on behalf of each party as they bickered over an outside commercial deal. Strong independent companies and intense competitors can stand in the same room only for so long before they start beating each other up.
The fear, he said, was of the project losing impetus, as it did in 1999.
This time, there were some big differences. It was a determined team with a common attitude working towards a structured goal. They had agreed on the company's capital structure and the commercial value of each party.
There was an almost tangible thread running through the deal: Keep up the speed, keep the momentum going and if there is a point where some farmers dig in their heels, charge on regardless.
And there was the brilliant idea of avoiding New Zealand's anti-competition watchdog.
"You don't go to the Commerce Commission and say, 'We are looking at a merger', you go to the Government and say, 'We want you to decide how NZ is going to interact on the international market'.
"To solve the merger between two companies which appears to be a contravention of the Commerce Act you need to call on the fact that this was not an ordinary merger - this is the way in which New Zealand's economy is moving."
Legislation was needed to make the deal possible.
At the time, the Government was tired of the industry's sand-kicking. The Minister of Agriculture, Jim Sutton, had seen many promises.
"When we gave him the merger agreement, he was pleasantly surprised. He then called our bluff by saying, 'If you want Government help, put your case in front of us by January 5 [last year]'."
That ultimatum was given in late December.
Mr Bowler had to persuade the Government to sidestep one of New Zealand's sacrosanct legal planks to assist the domestic economy.
He presented a paper to Government executives arguing that the formation of Fonterra would be good for the economy.
The question, he said, was whether it wanted a "little-company country or a country prepared to make exceptions".
Commitment from executives of Global Dairy Company, as Fonterra was then called, was impressive. All questions raised by Government officials were answered.
Compromises were made, including a regulatory structure that gave ease of entry to new players and restrained Fonterra's competitive hold over the market.
"Labour did take us seriously. They took a holistic view and thought of it as industry restructure, rather than competition."
It was a final sprint to get legislation in place, with a nod from the select committee in time for formation of a new company by the new financial year.
But there was no champagne and caviar. "I don't want to sound too goodie-two-shoes, but there was about two minutes of congratulations. We were simply too exhausted."
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