After just 88 days in Gov. Bruce Rauner’s administration, former Illinois Policy Institute head Kristina Rasmussen is out as the governor’s chief of staff — leaving a job she said she knew would be “rife with promise but would come with a lot of turbulence.”

Rauner credited her with “outstanding work” in “very challenging, wild times.”

Her departure comes just a week after Rauner signed House Bill 40, a controversial abortion trigger law, which Rasmussen and many other conservative Republicans vehemently oppose.

She will be replaced by Rodger Heaton, the governor’s director of public safety and Homeland Security adviser. Heaton takes charge on Monday.

The governor announced Rasmussen’s exit on Friday. In a staff phone call, Rasmussen said she’s leaving to start an initiative focusing on an anti-union, right-to-work case that Rauner pioneered that is now heading to the U.S. Supreme Court. She will remain on the governor’s staff until next Friday, “to help ensure a smooth transition.”

Rauner in the call said Rasmussen was leaving “to pursue her dream, a very exciting opportunity.”

“You’ve done outstanding work for the months that you served. Very challenging, wild times, and we appreciate it,” Rauner said.

Rasmussen recalled being called to take over as chief of staff, saying she was “a little taken back” and knew that it was “rife with promise but would come with a lot of turbulence.”

“I’m going back into the private sector to lead a new initiative that will leverage one of his other greatest victories, that of the Janus v. AFSCME fair share case that was just picked up by the United States Supreme Court,” Rasmussen said during the call. “So whether we are inside of government or outside of government there’s so much opportunity for us to change policy and change lives for the better. ”

Rasmussen said she had “two key responsibilities” during her tenure: to “refresh the staff” and to deal with the school funding crisis.

“As I look back now, to three months in, I can say with great pride that I discharged both of those duties faithfully with your help,” Rasmussen told staffers.

Rauner called his new chief of staff a “superstar.” That’s a term he’s called many former staffers and appointees, many of whom are no longer within the administration, including former chief operating officer Linda Lingle, education secretary Beth Purvis and budget adviser Donna Arduin.

Rodger Heaton. Illinois Department of Transportation Photo.

On the call, Heaton credit Rasmussen with building a “terrific team.”

“That was a difficult job to do at a mid point of the administration. … I think you’ve put a great team together.”

Despite the negative perception of such a short term — with Rauner in crisis mode during most of that time — the governor in a statement said Rasmussen had “delivered on all fronts.” He said she made “significant improvements” … “in a very compressed and challenging time.”

Although Michael Lucci, also a former Illinois Policy Institute staffer, remains in the administration’s policy department, no other top posts remain filled by members of the conservative think tank. The group’s current CEO John Tillman, once a close friend and adviser to Rauner, dubbed the governor “Benedict Rauner” in a Facebook post last week for signing the abortion bill.

He also sounded off on Rasmussen’s exit on Friday, while crediting her for her work with “the three biggest accomplishments the Rauner campaign cites,” including the Janus right to work case; right-to-work in Lincolnshire and in helping to get a private tax school scholarship into a school funding bill.

But Rauner’s former ally also took a shot at the governor and first lady Diana Rauner: “Regarding the governor’s office, organizational culture starts at the top and it is my hope that the governor reflects on the events of the last two years, is self accountable and finally has found a chief of staff that can work within the rather unusual dynamics he and his wife create,” Tillman wrote on Facebook.

“…As to whether this governor can turn his administration around, the jury is still out and the odds are long,” Tillman wrote.

The Rauner administration shakeup began July 10 when Rauner unexpectedly fired his chief of staff, Richard Goldberg. Goldberg was swiftly replaced by Rasmussen, former president and CEO of the Illinois Policy Institute. That sparked the exits of at least 20 employees, many of whom left because they didn’t believe in the direction the governor was taking in hiring members of the conservative think tank.

The staff changes came after Rauner vetoed a state budget that included an income-tax hike, only to see his veto overridden with the help of several Republicans.

A series of embarrassing flaps followed the staff shakeup. Rauner fired his “body man” on his first day after his homophobic and racially insensitive posts were found on Twitter. The governor also was criticized for his response to Lake County flooding and his failure to call it a disaster area earlier.

The governor defended his hires this summer. In July, Rauner said he was working to assemble “the best team in America.” He also declared “change happens” and described criticism of his staff shakeup as “political spin baloney.”

But then came more changes. The governor ousted four members of his new communications team — two of them former Illinois Policy Institute staffers — in August amid a statement regarding a cartoon the think tank posted.  The statement cited Rauner’s position as a “white male” as a reason not to comment on the cartoon, which some critics dubbed racist.  And soon after, the governor’s general counsel Dennis Murashko was out the door.

The series of departures left many scratching their heads as to what was truly going on behind the revolving doors.

“What’s more embarrassing for Rasmussen and the IPI gang is they inherited an easier situation than the previous team had to manage because the budget was done,” said a political strategist who did not want to be named. “No more daily crises of government on top of the typical daily grind, and they couldn’t even handle that.”

The strategist said Rauner’s former team managed a bevy of daily crises, including managing the media and the GOP caucuses with no budget in place, a war with AFSCME, and gripes with Mayor Rahm Emanuel and Illinois Comptroller Susana Mendoza.

Others saw the shift as a sign the governor realized he erred in his ways: “It only took three months for Bruce and Diana to admit they made a massive mistake,” another political operative said.

Rauner’s new chief of staff is a former U.S. attorney for central Illinois. Besides serving as Rauner’s public safety director and Homeland Security advisor, Heaton also was chairman of the Statewide Commission on Criminal Justice and Sentencing Reform.

“I’m excited to promote Rodger to be our team leader,” Rauner said. “His combination of legal, legislative and policy experience will help us build on the significant improvements that Kristina accomplished in a very compressed and challenging time.”

In the call to staffers, Heaton said, as chief of staff, he’d focus on the “structural reforms” Rauner has been fighting for.

“We’re still committed to the structural reforms that you’ve been talking to the people in the state for years now. There is a lot of work to do, and I think Kristina is right, it’s going to be a challenge for us in some respects. But I think this is a team that can get it done,” Heaton said.