Inside the Department of Homeland Security after the purge

What had been viewed as a done deal was suddenly in jeopardy after the White House sent a letter to a Senate committee saying Vitiello's nomination was being pulled.

That was news to both Vitiello and Nielsen. For nearly 12 hours, DHS officials scrambled to make sense of what the White House was up to. ICE leadership was under the impression, even that next morning, that it was a clerical error, according to someone with knowledge of the nomination process.

But then, around 10 a.m., President Donald Trump, on his way to California to visit the border, confirmed that he was moving in a "tougher" direction and that Vitiello's nomination was indeed killed.

The White House never called Vitiello to tell him, according to a senior DHS official.

The surprise withdrawal of Vitiello's nomination not only revealed a disconnect between DHS leadership and the White House, it also foreshadowed a coming purge. Over the next week, a succession of high-profile departures rippled through the upper ranks of DHS, including the forced resignation of Nielsen, as well as her acting deputy Claire Grady, who's spent years working in government.

After being passed over for the top job in favor of Customs and Border Protection Commissioner Kevin McAleenan, Grady stepped down. Her post has since been temporarily filled by Transportation Security Administration Administrator David Pekoske.

As career officials have departed, and deputies moved into new leadership positions, more than half of the department's top roles are now filled by temporary leaders.

More change could still come. Amid the shakeup, there were rumors that at least two other top DHS officials, US Citizenship and Immigration Services Director Lee Francis Cissna and DHS General Counsel John Mitnick, could possibly be pushed out of the administration.

According to interviews with a number of current and former officials, the recent purge has left department leadership in a state of limbo even as it's charged with containing the worsening situation at the border in a way that pleases the President. The reshuffling is compounded by the fact that DHS has been plagued by years of low morale, ranking last in 2018 among large agencies for employee engagement.

It also comes as employees move into a new DHS headquarters in southeast Washington DC, which is the former site of a psychiatric hospital.

"The shock and way it went down will have a lasting effect, in that people won't easily forget," said an administration official.

Asked about the effect the shakeup might have on employee morale, one DHS official said, at headquarters "there's been impact.

Since becoming acting secretary, McAleenan has brought about a half dozen people from CBP with him to headquarters, according to an administration official. The official told CNN that McAleenan spent last week holding meetings with senior staff and departmental heads and talking about his plans, which are "in line with where Secretary Nielsen was."

The source said McAleenan will likely keep his focus on immigration and border security. In perhaps a demonstration of that: His first official trip as acting secretary was to McAllen, Texas, which has seen a surge in illegal border crossings this year.

Meanwhile, McAleenan's new deputy, Pekoske, is "trying to understand" the rest of the department outside of TSA. Pekoske also served as a former vice commandant of the US Coast Guard.

"There's a learning curve for all of the staff that support the leadership," said a senior DHS official. "It's not like a complete stranger coming in, but there's a settling that needs to occur. It will take time."

A former DHS official noted that a leadership change of this magnitude would likely disrupt decision making. "When there's shakeups at the top, what tends to happen is a lot of the decision-making grinds to a halt," the source said. "Everybody takes the foot off the gas a little bit and waits for the new team to arrive."

The former DHS official added that they've been recently contacted by people within DHS about exploring opportunities outside of the department. It's not clear how much changes at the top have factored into those decisions.

"There's no question that this kind of turmoil is going to be bad for morale," said Max Stier, CEO of the Partnership for Public Service, which produces the annual "Best Places to Work in the Federal Government" rankings. "Turnover, especially unplanned and chaotic turnover is consequential and will serve as a distraction away from the day-to-day job."

Under the DHS umbrella, one agency that saw improvement last year was the US Secret Service. That uptick happened under the leadership of Randolph "Tex" Alles, who's firing became public the the day after Nielsen resigned.

"Here's a leader who was turning things around at the Secret Service and this is likely to disrupt that change," Steir said.

Since its founding after 9/11, when 22 separate government agencies were combined into one, DHS has struggled to sort out its complicated management structure and establish itself as an effective Cabinet level agency, according to a 2018 Government Accountability Office report.

A 2019 GAO report however found that DHS had recently made considerable progress in addressing those issues. The leadership change could stall that.

DHS has been thrust to the forefront of many of Trump's most controversial policies, including "zero tolerance," which resulted in the separation of thousands of families at the border. DHS also bore the brunt of the recent government shutdown, as thousands of TSA agents, ICE agents, CBP officers and others were forced to continue going to work without pay.

"You have federal employees feeling like they are being blamed for the country's problems, that our agencies are part of the problem -- or that our political leadership in the administration and on the Hill don't really understand or value what we do," said Michael Knowles, president of the labor union that represents DC-area employees at the USCIS, which oversees lawful immigration to the US.

"You don't fix it by changing who leads the agency, you still have the same laws and procedures," he added.

Two more officials - Lee Francis Cissna and John Mitnick - have had their disagreements with the White House over immigration policy and were reportedly on the cusp of being forced out as well.

As the top lawyer inside DHS, it fell to Mitnick to push back against the White House on a proposal to release undocumented immigrants into sanctuary cities, which DHS lawyers killed.

In February, according to documents obtained by CNN, Mitnick told the White House in writing that such a move could only be done if there was a "strong, mission-related rationale" pertaining to the responsibilities of DHS.

As of Wednesday, Mitnick was still in his role.

The relationship between the White House and Cissna, who volunteered for the Trump campaign, also appears to have taken a turn for the worse sometime last fall.

There has been "growing frustration" in the administration that USCIS is "not moving fast enough, going far enough" with the authorities it has, according to an administration official.

Last fall, Cissna got in a shouting match on a conference call with a senior White House official, who was urging Cissna to take a stronger stance on illegal immigration and asylum reform, according to a source familiar with the situation.

A USCIS official sought to tamp down reports of any tension with the White House.

"USCIS Director Cissna is relentlessly focused on advancing President Trump's agenda forward to the maximum extent permitted under the law and to say otherwise is false," said a USCIS official in a statement.

Cissna's supporters came to his defense when rumors began to circulate last week about his imminent departure. Republican Sen. Chuck Grassley spent days urging the White House not to fire Cissna. "It would be a huge mistake for the administration to get rid of Director Cissna," said Rosemary Jenks, director of government relations at NumbersUSA, a group that supports reduced immigration.

Despite changes in the ranks and the roll out of aggressive immigration policies -- many of which have been blocked by the courts -- there continues to be an increase of migrants arriving at the southern border.

The challenge hasn't gotten easier for McAleenan. When he was CBP commissioner, the President told McAleenan he would pardon him if he were sent to jail for having border agents block asylum seekers from entering the US in defiance of US law, senior administration officials tell CNN.

More possible disruptions may be on the horizon for the department as it tries to settle into its new normal after a week of upheaval.

But for now, the department appears to be trying to move forward as best it can, even under the uncertainty of who will helm it, and some of its agencies, next.