“It is undisputed, using the primary source upon which the Government itself relies, that these six countries have overwhelmingly Muslim populations that range from 90.7 percent to 99.8 percent," he wrote. "It would therefore be no paradigmatic leap to conclude that targeting these countries likewise targets Islam. Certainly, it would be inappropriate to conclude, as the Government does, that it does not."

The plaintiffs pointed to comments made by Trump’s own adviser Stephen Miller to argue that both versions of the travel ban are “fundamentally” similar and would have the same impact.

“Fundamentally, you’re still going to have the same basic policy outcome for the country, but you’re going to be responsive to a lot of very technical issues that were brought up by the court and those will be addressed,” Miller told Fox News last month. “But in terms of protecting the country, those basic policies are still going to be in effect.” 

The administration urged the court not to read into “secret motives” or the “veiled psyche” of policymakers, and said there is a difference between statements made by a candidate and an elected official. 

But Watson vehemently pushed back, saying there is nothing is nothing "‘secret' about the Executive’s motive specific to the issuance of the Executive Order.”

He pointed to Trump’s comments on the campaign trail, top ally Rudy Giuliani’s explanation of the order and a press release titled “Donald J. Trump is calling for a total and complete shutdown of Muslims entering the United States.”

“Any reasonable, objective observer would conclude, as does the Court for purposes of the instant Motion for TRO, that the stated secular purpose of the Executive Order is, at the very least, ‘secondary to a religious objective’ of temporarily suspending the entry of Muslims,” Watson stated.

The Department of Justice said in a statement that it "strongly disagrees" with the ruling, calling it "flawed both in reasoning and in scope."

"The President’s Executive Order falls squarely within his lawful authority in seeking to protect our Nation’s security, and the Department will continue to defend this Executive Order in the courts," the DOJ said.

In determining that Hawaii has legal standing to bring the lawsuit, Watson ruled that it demonstrated that the state’s educational institutions and booming tourism industry would suffer as a result of the policy.

The administration had sought to chip away at states’ cases by clarifying that the ban does not apply to legal U.S. residents and those who already hold a valid visa to come to the U.S. The retooled order also offers a lengthy list of examples of who can qualify for a waiver.

In Wisconsin, a federal judge already agreed to issue a narrow, temporary hold to prevent the policy from applying to a Syrian refugee and his family.

The refugee was granted asylum and fled to the U.S. in 2014, but he is working to bring over his wife and daughter, who are still living in the war-torn city of Aleppo.

U.S. District Judge William Conley, an Obama appointee, ruled that the plaintiff’s lawsuit over the new ban shows some likelihood of success based on the merits of the case because his family faces “significant risk of irreparable harm” if they stay in Aleppo. 

Federal judges in Maryland and Washington state also heard arguments on separate lawsuits challenging the travel ban on Wednesday. 

In Seattle, where the first nationwide freeze was placed on Trump’s initial order, a group of states led by Washington was pushing to have the previous restraining order apply to key portions of the revised order.

But U.S. District Judge James Robart, a President George W. Bush appointee, said the orders were substantially different and intended to deny the motion, according to multiple reports.

Asked by The Hill about the judge's ruling, Speaker Paul Ryan (R-Wis.) said he was confident Trump's travel ban would stand up in court.