Is University of California President Janet Napolitano attempting to scapegoat two of her top aides for a scandal that enraged the California Legislature? Or were the aides’ abrupt resignations last week a Napolitano message to regents and lawmakers that she realizes the gravity of the mistakes made by the UC Office of the President in interfering with an audit ordered by the Legislature?

This was the speculation touched off by Wednesday’s UC announcement that Seth Grossman, Napolitano’s chief of staff, and Bernie Jones, his deputy, had “resigned to pursue other opportunities.” Neither offered substantive comments to the media on their decisions.

Jones played a central role last year in getting three UC campuses to change their responses to state Auditor Elaine Howle, who had been asked by the Legislature to examine campuses’ relationships with Napolitano’s office – the latest of several attempts in recent years by the Legislature to get a better understanding of UC’s murky finances.

The responses were supposed to be confidential so Howle could get an unfiltered assessment of UC’s Office of the President. But at Jones’ direction, officials at UC Santa Cruz, UC San Diego and UC Irvine either dropped criticism or offered more positive descriptions.

The San Francisco Chronicle, which in May broke the story that emails confirmed interference with the audit, reported that Jones’ boss – Grossman – was CC’d on emails about responses to the audit and that Napolitano’s involvement in the attempt to protect her office’s reputation was direct and indisputable.

UC Santa Cruz’s initial response to Howle’s inquiry was perhaps the harshest of any campus. It rated the help from Napolitano’s office in four categories as either “poor” or “fair.” All were later changed to “good.” Ratings for three other services were changed from “good” to “exceptional.”

Santa Cruz response changed after Napolitano spoke with chancellor

The changes were undertaken in November 2016 – after Napolitano spoke with UC Santa Cruz Chancellor George Blumenthal.

“Per your conversation with Chancellor earlier today, we have already started the recall process of the State Audit Survey,” Ashish Sahni, Blumenthal’s top aide, told Napolitano in an email obtained by the Chronicle.

The resignations of Grossman and Jones were only the latest fallout from the spring scandal. After Howle told legislators she’d never seen such improper behavior from a state agency in her 17 years as auditor, they passed a bill making it a crime subject to a $5,000 fine to interfere with a formally requested state audit. Gov. Jerry Brown signed it into law last month.

Meanwhile, at the behest of UC regents, former California Supreme Court Justice Carlos Moreno continues to conduct an independent investigation into the scandal. There is no indication when he will submit his report; it is not on the agenda for the regents’ meeting in San Francisco on Wednesday and Thursday.

Moreno’s inquiry has so far seemed a low-profile, leak-free effort. But at the very least, it has the potential to embarrass Napolitano again over her handling of the scandal.

Howle – who discarded the campuses’ responses as worthless because of the interference – released the audit on April 25. The finding that initially spurred the most headlines was Howle’s assertion that the UC Office of the President hid $175 million in funds from regents and the public.

Napolitano was able to lessen the fallout from that finding by arguing that far from being hidden, the funds were dedicated to important programs.

But her assertion that audit responses were changed after individual campuses’ asked for help from her office were immediately challenged by state lawmakers at a contentious May 2 hearing. Less than 30 hours later, the Chronicle posted its story showing the changes had been orchestrated by Napolitano’s office – not initiated by the campuses.

At San Diego State and UCLA, the responses to an aggressive gambit by conservative activist David Horowitz were noticeably different. Horowitz distributed a poster that can be filled out to identify supporters of the Boycott Divestment Sanctions movement, which targets Israel, as “pro-Palestinian terrorists.” Horowitz rejects the idea that this is an extreme tactic, saying campus groups which back BDS also support Hamas, which is officially recognized by the State Department as a terrorist group.

When seven San Diego State students were so identified with the inflammatory posters in April, San Diego State University President Elliot Hirshman and his administration met with upset students. The subsequent statement issued by the university said a committee would review university policies with the goal of “balancing freedom of expression and protection from harassment.” But the statement alluded to the posters, however hateful they may be, as falling under the First Amendment — political speech with “protected status.”

This led to a protest in which dozens of students surrounded a car that Hirschman was in and wouldn’t let it leave. After an hour, Hirschman got out and spoke with the students. But they remain unsatisfied and have called for the SDSU president to resign. He also faces faculty criticism.

UCLA warned of legal action against Horowitz

At UCLA, the fliers — which named faculty members as well as students — triggered a much stronger response. In an email to campus students, faculty and employees, Jerry Kang, vice chancellor for equity, diversity and inclusion, said the tactics “amounts to a focused, personalized intimidation that threatens specific members of our Bruin community,” Kang said in the email.

The Daily Bruin reported that Kang said “UCLA will enforce university policies on harassment and intimidation by pursuing legal action against Horowitz.”

Horowitz responded by threatening to sue Kang for defamation. He also accused UCLA of double standards and hypocrisy — a view also voiced by high-profile UCLA Professor Judea Pearl, who said even the word Israel “has been shunned by the UC administration like leprosy.”

Now it’s UC Irvine’s turn for unrest.

On May 18, about 50 protesters disrupted the screening of “Beneath the Helmet,” a documentary about Israel soldiers, an event that was to include a discussion between students and former Israel soldiers. After protesters blocked exits, UCI police intervened and led those in the screening room to safety amid what witnesses described as a hail of profanity and anti-Israel chants.

UC Irvine Chancellor Howard Gillman emailed students, faculty and employees the next day, saying the protesters “crossed the line of civility.”

UC Irvine was the scene of perhaps the best-known U.S. campus protest against Israel. In February 2010, 11 UC Irvine and UC Riverside students repeatedly disrupted a speech by Michael Oren, then Israel’s ambassador to the U.S.  In 2011, 10 of the students were found guilty of misdemeanor counts of organized disruption of the event. They were ordered to do 56 hours of community service and serve three years of “informal probation.”

Orange County District Attorney Tony Rackauckas’ decision to pursue criminal charges over and above the mild discipline the students faced on campus was sharply criticized by Erwin Chemerinsky, dean of UC Irvine’s law school. He said it was “unnecessarily divisive.”

Recent events have shown what hooey this is. It’s not just the crown jewels of the UC system — the Berkeley and Los Angeles campuses — that continue to thrive. It’s also the lesser-hyped schools:

The Orange County Register notes an honor for UC Irvine.

“As the University of California, Irvine approaches the milestone of its 50th year of operation in 2015, the campus has been honored again by Times Higher Education magazine as the top-rated university in the United States for schools under 50 years old.”

To the south, UC San Diego continues to stake out a global reputation as a leader in biotech and the increasing integration of health care and nanotechnology.

It’s also just an outstanding all-around university. Overall, the school is ranked the 39th-best in the nation in the latest U.S. News and World report rankings.

But in its core specialty — life sciences — UC San Diego is ranked seventh-best in the world. This ranking is only likely to rise as the La Jolla area builds on its reputation as a global biotech-nanotech innovation hub.

Finally, out in the Inland Empire, there is UC Riverside, a campus that rarely gets much love from anyone.

Until now.

As the Sacramento Bee reported this week, in a Time magazine analysis based on Obama administration standards unveiled last year, the Riverside campus gives students the best value for their tuition based on “metrics such as graduation rate, tuition costs and percentage of students who receive Pell Grants, the federal low-income scholarship, to determine which schools offer the best value.”

The Time list puts UCSD second, UC Irvine fourth and UC Davis sixth.

All that budget misery seems to agree with the UC system.

Or rather, all that alleged budget misery seems to agree with the UC system.