On Australia Day 2007, scientist Tim Flannery was named Australian of the Year at a ceremony on the lawns of Parliament House. “He has encouraged Australians into new ways of thinking about our environmental history and future ecological challenges,” declared then-prime minister John Howard as he presented Flannery with the award.

For The Australian, this was too much to take. In its news story, the Oz reported Howard as having “embraced his inner greenie”, and in its editorial said the decision would be “a controversial choice for some”.

In the year that followed, The Australian published 72 pieces that were either about Flannery or mentioned him — many of them negative or disparaging, often describing him as a climate “alarmist”.

But it wasn’t until 2011, when he was named commissioner of the Climate Change Commission by the Gillard government, that Flannery felt the full force of The Australian’s aggression. “Professor Flannery, a mammalogist and a paleontologist, is no expert on global warming and has made a hash of the subject in the past,” the paper editorialised in February 2011. “Do we really need Professor Flannery to explain climate change? If he wants to be useful, he should urge the government to start selling uranium to India, pronto.”

Until the commission was scrapped in 2013, almost every story about him referred to Flannery’s “tax-payer funded” salary. It was used as an example of the excesses of the Gillard government’s spending in an editorial on September 20, 2013: “The cutting of former chief commissioner Tim Flannery’s $180,000 part-time salary for spruiking climate alarmism is a stark signal of a return to evidence-based and practical policy”.

In 2011, when he first started in the role, another editorial said Flannery was “not a bad bloke, but he would not have been our choice for climate commissioner, a three-day-a-week job for which he will be paid $180,000 a year”. That’s not to mention all the news stories including the same piece of background.

In August 2011, the paper published a story claiming that Flannery, who owned a house on the Hawkesbury River north-west of Sydney, had been scaremongering oldies out of their sea-level homes to drive down prices. The article, “Do as I say, not as I do: Flannery’s all at sea”, claimed Flannery had been preaching around the country on his cause: “A few years ago, he spoke of sea-level rises of biblical proportions, where walls of water eight storeys high would subsume all beneath,” the paper reported. “Given all that, many have been surprised to learn Professor Flannery has his own pile right on the water in the trendy tidal region of the lower Hawkesbury River, north of Sydney.”

The report quoted an online forum that had a post saying “doomsayers such as Professor Flannery, after having frightened the elderly to sell their seaside properties, are buying them”. The accusation was wrong and The Australian eventually published a correction a few days later after Flannery hired a QC to apply pressure.

One of the paper’s main allegations against Flannery was based on his comments in 2005 and 2007 that if climate patterns continued there could be trouble with Sydney’s water supply. And in 2007, speaking to the ABC, he referenced a report about increased evaporation rates. He says the point he was making was that we couldn’t assume dams would fill as they previously had — not, as The Australian reported, that the dams would dry up. Flannery insists he was being taken out of context, such that the paper could portray him as an alarmist or fanatic (which became a common feature of its descriptions of him).

In 2015, then-editor-in-chief Chris Mitchell summarised his view of Flannery when he told his own paper that The Australian’s Graham Lloyd was the smartest environment writer in the country “by light-years” and could “run rings around clowns like Tim Flannery in any forum on knowledge of the science”.

Becoming Australian of the Year in 2007 was “the critical point for their campaign against me,” Flannery told Crikey. “And it very much intensified when I became the climate commissioner. It’s sort of relentless really. The stories are so poorly written and so confusing it’s almost remarkable. I think they’ve done themselves an enormous disservice.”

Flannery, a passionate, internationally recognised scientist and author, acknowledges that if you want to create change “you’ll create many enemies”. But in the case of Australia’s national broadsheet, he says, “they take any opportunity to belittle, besmirch, denigrate in any way they can”.

TOMORROW: The man behind the Holy Wars