Political life changed dramatically for Morrison this week. Whether Joyce's elevation will benefit or harm the government at the election is an open question, but right now it is a massive complication for the PM.

It's unleashed a battle over power within the Coalition, and it's intensified the perennial difficulties on climate policy.

The surreal backdrop in this final week of Parliament before the winter break was Morrison quarantined at The Lodge, looming "virtually" over House of Representatives members, while Joyce, following his Tuesday swearing in, occupied the PM's chair at the centre table, the focus of attention.

To say the least, the symbolism was unfortunate. As Morrison said in another context, nothing beats being face to face. Being on a screen, upstaged by your unpredictable new right-hand man, is an especially unhappy place.

Behind the scenes, Morrison and Joyce negotiated the terms of their partnership. In the open, the restored leader let the Nationals run riot, in a way we haven't seen for a long time.

In the Senate on Wednesday, and then in the lower house on Thursday, Nationals moved amendments on water, challenging the Murray-Darling Basin plan, in an open split with the Liberals.

The water ploy was a gesture, and the revolt had been in the pipeline for months - and would, its proponents say, have gone ahead under Michael McCormack.

But for Joyce it was a convenient message to Morrison: the new leader is willing, if need be, to fight dirty to get as much as he can of whatever he wants.

Morrison's problems on climate policy, hard enough before, have just increased substantially. And indeed, so has the internal dilemma the Nationals face on the issue.

Previously it was thought McCormack and deputy David Littleproud might be open to some deal so Morrison could embrace the target of net zero by 2050 (firming his present stance of reaching net zero "preferably" by 2050).

But Joyce has a history of opposing a 2050 target. Despite this, Littleproud (who remains deputy) continued this week to signal that he could see a deal. That's a very odd situation.

In prime ministerial circles they remain hopeful of a deal, on the basis that Morrison and Joyce are pragmatists and money can smooth the way.

But opposition within the Nationals to the 2050 target was one important driver of the Joyce coup. If he did a backflip, that would anger many followers. He's privately been sticking to his position this week.

In an exercise that had critics quickly recalling Joyce's $100 roast during the carbon debate under Labor, Nationals senator Matt Canavan, a confidant of Joyce, conjured up a spectre of net zero in the cattle industry.

"Every cow emits about 2300 kilograms of carbon dioxide-equivalent gases a year," Canavan wrote in The Australian. "The CSIRO estimated last year that to reach net zero emissions, we would need to start with a carbon price of $30 a tonne now. Even a relatively small cattle producer runs about 1000 head. So they would be up for a $70,000-a-year cost under a net-zero policy.

"By 2050, the price would rise to more than $200 a tonne, taking the carbon bill on your steaks to a whopping $400,000 per year, per farm."

Canavan will be a significant player in the months ahead, and in the climate debate. Formerly resources minister, he has not sought to return to the ministry. Potentially he is both an influence on Joyce (he once worked for him), and also, as a backbencher, a tosser of grenades to remind the Liberals of the Nationals' clout.

Unless Joyce shifts his position, Morrison surely can't endorse the target. Joe Biden and Boris Johnson may or may not understand the concept of being "Barnaby'd".

While the Joyce coup has transformed the dynamics within the Coalition, it wasn't the worst thing confronting Morrison this week. That remains Covid and the flawed vaccine rollout. For all the numbers the government sprouts, the public are frustrated and weary and many people are worried.

The latest outbreak in NSW has seen fresh border closures and on Friday lockdowns for certain areas, including the City of Sydney, were announced. Special arrangements were required on Thursday to get the state budget passed. Premier Gladys Berejiklian said: "Since the pandemic has started, this is perhaps the scariest period that NSW is going through."

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Covid even wormed its way into the Barnaby story, with Joyce briefly absent at the start of Thursday's question time because he thought he might have been a contact of a close contact (he was quickly given an OK).

The rollout is still blighted by a shortage of supplies of Pfizer, hesitancy about vaccination in general and resistance to AstraZeneca in particular, and inadequate availability of convenient vaccination points.

Even limited outbreaks are disruptive, costly and unnerving, and there is always the danger of a major one occurring.

It may be, however, that the recent appointment of Lieutenant-General John "JJ" Frewen as Covid tsar is starting to improve the efficiency of the rollout. He's asking a lot of questions, and bringing in some of his own logistics people to help with the organisation.

Frewen's task, while waiting for more Pfizer supplies, is to get the rollout architecture into better shape. This includes improving communication with the public and relations with the states, and ensuring there are more channels for delivering the vaccines when extra doses arrive.

A lot is now riding on Frewen's performance. But, inevitably, not all the federal health bureaucrats are happy to find their patch taken over by the military man. It's another power struggle in Canberra.