WASHINGTON (AP) ― Homeland Security Secretary Janet Napolitano announced her resignation Friday to take over the University of California system, leaving behind a huge department still working to adjust to the merger of nearly two dozen agencies after the Sept. 11, 2001, terrorist attacks against the U.S.

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. 

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, a leading Democrat from New York, said Friday he wants 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 in Congress, she did not mention terrorism or the Sept. 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.