Fallout from the scandal over the firing of Rutgers University’s cantankerous basketball coach continued this past week as officials announced the resignation of the school’s top in-house lawyer and the start of an internal probe of the affair.

Senior vice president and general counsel John Wolf — part of the decision-making team that kept Mike Rice on staff despite mounting evidence of his abusive conduct toward players — is being replaced, at least temporarily, by Rutgers Law School-Newark Dean John Farmer Jr.

The university had said earlier that Wolf would stay on as a staff attorney while giving up the top legal job, but on Thursday it announced he would leave “in the best interests of the university.” Wolf, who had served in Rutgers’ legal department in various capacities since 1984, agreed to work with the new general counsel to assure a smooth transition.

Rutgers President Robert Barchi said Farmer, a former state attorney general, will serve in his new position for 12 to 18 months to help the administration manage, among other things, the impending July 1 integration of Rutgers and the University of Medicine and Dentistry of New Jersey. During that period, Ronald Chen, the current vice dean of Rutgers Law School-Newark, will be acting dean.

The internal investigation will look at “circumstances surrounding the inappropriate behavior in the men’s basketball program and how they were addressed, and … make recommendations on how we can improve,” Barchi and Board of Governors Chairman Ralph Izzo said last Monday.

Who will carry on the investigation and whether that person will be a lawyer is not yet determined, university spokesman Greg Trevor said. He declined to say whether the probe would cover actions of any of Rutgers’ previous advisers in the matter.

Also made public last week was an agreement detailing the financial terms of Athletic Director Tim Pernetti’s April 5 resignation in the wake of the scandal.

The university treated his departure as a termination without cause and agreed to pay his $453,000 annual salary through June 30, 2014, in addition to any bonuses due and outstanding travel or business expenses. Within 30 days of the agreement, Pernetti also is to receive a payment of $679,500 — equal to 18 months’ salary. 

Rutgers agreed it would not “criticize, denigrate, or disparage Mr. Pernetti in any manner whatsoever” or “make any comments or statements to the press or any other individual or entity that may likely adversely affect Mr. Pernetti’s reputation.” 

Pernetti agreed to withhold criticism and to cooperate with the university, but he is permitted to “truthfully discuss” the matter.

Each party must pay its own fees in the event of a dispute over the contract, which must go to arbitration, but the university promised to indemnify Pernetti in the event of litigation.

The indemnity provision came into play right away, as fired Director of Player Development Eric Murdock is suing Pernetti — as well as Barchi, Rice and the university — claiming he was wrongfully terminated for speaking out about Rice’s conduct.

Murdock’s lawyer, Barry Kozyra of Kozyra & Hartz in Roseland, contacted the university on Murdock’s behalf last July 11.

Murdock’s contract had expired shortly before the letter —  an effective termination, he claimed, in retaliation for discussing Rice’s misconduct. 

Pernetti enlisted Wolf to retain outside counsel to respond.

He contacted Jackson Lewis in Morristown. Partner John Bennett wrote to Kozyra on July 19, requesting production of evidence to support the allegations of Rice’s misconduct.

In a Sept. 26 letter, Kozyra indicated he had completed his preliminary investigation and requested a meeting.

The Nov. 26 meeting was attended by Pernetti and Richard Cino, managing partner of Jackson Lewis’ Morristown office. Kozyra showed a 30-minute video of clips of Rice during practices spanning the 2010, 2011 and 2012 seasons, which showed him shoving and throwing basketballs at players and using off-color language.

The next day, Wolf retained John Lacey, of Connell Foley of Roseland, to investigate Rice’s conduct and Murdock’s claim.

Lacey submitted a report on Jan. 21 that attributed much of Rice’s behavior to a demanding coaching style. He acknowledged that rough physical contact with players and use of “faggot” and other terms “crossed the line” and reasonably could be interpreted to bring shame and embarrassment to the university in violation of his contract.

But Lacey said he could not conclude that Rice had created a hostile environment under New Jersey law.

According to Barchi, it was outside counsel who advised that Rice could not be fired for cause, though he did not specify whether it was Connell Foley or Jackson Lewis or both.

Lacey declines comment and neither Cino nor Bennett responded to a reporter’s calls.

In December, Rice was suspended for three games and fined $50,000. Pernetti claimed to have reached that decision himself, and Barchi agreed.

Barchi claims he didn’t see the video until April 2. Earlier that day, ESPN, who got the tape from Murdock, aired it. Barchi ordered Rice’s termination on April 3.

According to invoices retrieved via an Open Public Records Act request, the university has accrued a total of $75,783 in legal fees in connection with the Rice investigation and Murdock’s claims.

Connell Foley has been paid $64,604, charging $185 per hour for Lacey, $190 for firm partner Tricia O’Reilly and $145 for associate Meghan Burke.

Jackson Lewis has received $11,180, charging a $195 hourly rate for both Cino and Bennett.

Trevor did not respond to requests to identify Rutgers’ defense counsel in Murdock’s suit.

Kozyra did not respond to calls or emails.

Farmer was state attorney general from 1999 to 2002 and before that served in Gov. Christine Todd Whitman’s administration in various capacities, including chief counsel. Farmer was first chairman of the N.J. Domestic Preparedness Task Force and was a senior counsel and team leader for the National Commission on Terrorists Attacks upon the United States (the 9/11 Commission) and a principal author of its final report.