The former Arizona governor came to President Barack Obama's Cabinet with plans to fix the nation's broken immigration system, and she is leaving in the midst of a heated battle in Congress over how - or if - that overhaul will be accomplished.
The most frequent contact by most Americans is with the department's Transportation Security Administration screeners at airports. But its charter is much broader: It comprises agencies that protect the president, respond to disasters and enforce immigration laws as well as secure air travel. It includes the Secret Service, the Coast Guard, the Federal Emergency Management Agency, Immigration and Customs Enforcement and Customs and Border Protection as well as TSA.
Like the department Napolitano has run since the beginning of the Obama administration, the University of California system is a giant, multilayered organization, though with a far different mission. Her appointment, which still must be confirmed by the system's board of regents, could triple Napolitano's salary from $199,700 to around $600,000. She said she would stay on as secretary until early September.
It is not clear whom Obama may be considering to replace her.
Sen. Charles Schumer, R-N.Y., said Friday he wants to Obama to nominate New York Police Department Commissioner Ray Kelly.
Unlike the University of California school system, which dates to the 1860s, the Homeland Security Department is just a decade old and at times has seemed in search of a clear mission.
Though Napolitano came to Washington with plans to change the immigration system, her tenure is marked with few new sweeping immigration policies. And those she has pushed through were met with great controversy, such as a policy to give thousands of young immigrants living in the U.S. illegally temporary reprieve from deportation, a plan rolled out in the summer of 2012 before the presidential election.
Opponents assailed Napolitano and Obama for creating what they called "backdoor amnesty." Under her instructions, immigration officers have been told to focus on deporting criminals living in the U.S. illegally who pose dangers to public safety and national security.
When Napolitano took over as secretary, she was quickly faced with counterterrorism challenges outside her normal experience. During her first testimony as secretary on Capitol Hill, she did not mention terrorism or the 9/11 attacks in her prepared remarks. And after an al-Qaida operative nearly took down a commercial airliner over Detroit on Christmas Day in 2009, Napolitano went on national television and declared that the "system worked," a statement widely ridiculed.
But as the nation saw an uptick in attempted terror attacks in the first part of Obama's first term, Napolitano turned her focus to terrorism. She traveled around the world, strengthening information-sharing and travel-security policies with other countries. She launched a national ad campaign to alert the public to suspicious activity. And she scrapped the much-mocked color-coded terror alert system put in place after the 2001 attacks.
She also was at the helm during a number of controversies.
Secret Service officers and agents were accused of spending a wild night with various women, including some prostitutes, at a hotel where the employees were staying ahead of a presidential trip to Cartagena, Colombia. Eight of the Secret Service employees were forced out of the agency, three were cleared of serious wrongdoing, and at least two have fought to get their jobs back. The incident raised questions about the culture of the agency which Napolitano and her senior staff stood by consistently.
Also, one of Napolitano's appointees, a protegee from her time in Arizona, Suzanne Barr, was forced to give up her post as Immigration and Customs Enforcement chief of staff after being accused in a lawsuit of sexual harassment. In her resignation letter, Barr said she has been the subject of "unfounded allegations designed to destroy my reputation."
Before government-wide budget cuts earlier this year, Napolitano warned of hours-long waits at airport security checkpoints and customs lines, and a near standstill of cross-border traffic because of planned furloughs for Transportation Security Administration and Customs and Border Protection officers. At the start of the budget sequester, she even declared that customs lines at large airports, including in Los Angeles and Chicago, were already backing up. But the massive delays she predicted never materialized. Critics said she was fear mongering for political reasons.
Before budget cuts went into effect, the department also began releasing detainees from immigration jails, citing the impending budget woes. Napolitano and the administration initially said Immigration and Customs Enforcement had released only a few hundred people. The Associated Press later reported that internal department documents showed that more than 2,000 people had been released for budget reasons. Napolitano publicly rejected that report, saying it was "not really accurate." Days later, ICE Director John Morton told a House panel that 2,228 people had been released.
"Janet's portfolio has included some of the toughest challenges facing our country," Obama said in a statement Friday. "She's worked around the clock to respond to natural disasters, from the Joplin tornado to Hurricane Sandy, helping Americans recover and rebuild."
He said, the American people "are safer and more secure thanks to Janet's leadership in protecting our homeland against terrorist attacks."
She said in a statement, "The opportunity to work with the dedicated men and women of the Department of Homeland Security, who serve on the front lines of our nation's efforts to protect our communities and families from harm, has been the highlight of my professional career."
In California, she will take her new job as the university system grapples with growing student demand, tighter budgets and complaints about tuition that has nearly doubled over the past five years. She will succeed President Mark Yudof, who led the system through a tumultuous five years marked by unprecedented budget cuts, sharp tuition hikes, employee furloughs and rowdy campus protests. After several years of deep budget cuts, Gov. Jerry Brown earlier this month signed a state budget that boosts funding, but the system still faces serious financial challenges from rising costs for employee salaries, retirement benefits and other expenses.
Over the past years, the university system has significantly increased the number of out-of-state students who pay three times the tuition of in-state residents, prompting complaints that many top California students are being shut out of the most prestigious state campuses.