Barely before all the votes had been counted, Donald Trump was licking his wounds and seeking political cover.

“Congratulations to Roy Moore on his Republican Primary win in Alabama. Luther Strange started way back & ran a good race. Roy, WIN in Dec,” he tweeted. A few hours later, he followed up: “Spoke to Roy Moore of Alabama last night for the first time. Sounds like a really great guy who ran a fantastic race. He will help to #MAGA.”

In reality, the victory by Moore – a 70-year-old firebrand who defeated Strange, the candidate who Trump had endorsed and campaigned for – just made life a lot tougher for the President, who was said to be “embarrassed and pissed” that his man lost. He even deleted his tweets in support of Strange, presumably hoping nobody would notice.

Nine months into his presidency, Trump is flailing and struggling to move forward on the promises he made on the campaign trail. This week, the third attempt by Republicans to repeal and replace Obamacare fizzled and failed after it became clear they did not have sufficient votes.

Desperate for a win, the President and the Republican leadership in the House and Senate are pushing ahead with tax reform, and Trump has announced he plans a sweeping rewrite of the federal tax code – including the cutting of corporate tax rate from 35 per cent to 20 per cent.

His proposal will also lower the top income tax rate from 39.6 percent to 35 per cent: something many will see as a gift for the wealthiest in society.

Yet getting such legislation passed while juggling the nation’s budget faces many hurdles, including the opposition of conservative Republicans on Capitol Hill who want to see federal spending cut to the bone. In the past, they have shown they are willing to force a government shutdown to push their point.

Donald Trump says battling Atlantic Ocean in hurricane relief is difficult

The election to the Senate of a man like Moore, someone who has spent his career courting controversial issues and promoting himself as an anti-establishment individual, will only make things tougher for Trump and the Republican leadership.

That was why Senate majority leader Mitch McConnell poured so much money into Strange’s campaign, and why Trump and Vice President Mike Pence appeared alongside him in Alabama. The last thing they needed was another maverick who might be prepared to derail a bill if he chooses to – much in the way that John McCain killed off healthcare.

Jeanne Zaino, professor of political science at Iona College, said Trump may not suffer in the short term, but Moore’s win creates huge problems for the Republicans and their attempts to govern – underscoring the fracture within the party between its base and its leadership. And down the line, it will be an issue for Trump if he seeks re-election in 2020 with no legislative achievements.

“I don’t think it will bite him at this time, but it’s really bad for the Republicans and for trying to govern the country,” she said. She added that it also raised questions about the political counsel Trump received before agreeing to involve himself in the Alabama race, rather than waiting until a candidate had been chosen.

As it is, Trump has disappointed many of Moore’s supporters who voted for the President in 2016, and believe he should have either backed their man or else stayed in the White House.

And Moore’s win will only encourage other anti-establishment candidates and give succour to Steve Bannon, Trump’s former chief strategist who helped manage Moore’s campaign.

Bannon, grinning like a cat, popped up at Moore’s victory party in Montgomery, claiming fealty to Trump and saying the judge’s win was a victory for the President. Yet in a clear dig at Washington, he added: “Who’s sovereign, the people or the money? The people of Alabama just answered: the people.”

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Reports suggest Bannon is now planning to back a number of similar candidates in states such as Mississippi and Arizona, using the money of mega-donor Robert Mercer, the technology billionaire who helped fund Breitbart News.

In another blow to McConnell, Senator Bob Corker of Tennessee, Republican chairman of the Senate Foreign Relations Committee, used Tuesday to announce his retirement – a move that will likely trigger another bitterly fought race for his replacement.

Scott Reed, a political consultant for the US Chamber of Commerce, told The Washington Post that while Trump and Moore might appear to be like-minded individuals, the former judge’s presence in Washington will be less useful to the President now he is supposed to be trying to govern, rather than simply campaign.