"I think of everything in terms of a father and a coach," Jones said in an interview. "When you're talking about somebody that understands ethics, it starts with myself and our entire staff."
The complaint was filed February 9 in federal court in Nashville, two days after Manning led the Denver Broncos to victory in Super Bowl 50. The six accusers are not named in the complaint.
A "hostile sexual environment of rape by male athletes" was "condoned and completely unaddressed" by university officials from the chancellor down to the head football coach, the lawsuit said.
"As the leader, yes, it hurts," said Jones, the head coach since 2013. "You get angry ... I feel for the alleged victims but also I feel for our players as well ... because of all that's involved."
'In one second your life can change'
The lawsuit centers on five alleged rapes of female students reported between 2013 and 2015. The sixth accuser is a woman who says she was retaliated against for supporting another of the accusers.
"We came together to change what is done about sexual assault," one of the accusers, identified in the lawsuit as Jane Doe 1, said in a phone interview.
CNN's policy is not to name victims of sexual assault or rape.
The university denies a culture of sexual assault has thrived on the Knoxville campus.
Jones said there is an almost "daily dialogue" with players on how to treat women and a year-round personal growth and development program. And he prides himself on the academic success and graduation rate of his players.
"Like a parent, you're trying to educate them on great decisions," he said. "We call it the 'one-second rule' -- in one second your life can change by one decision and that's life. ... We talk about that every single day, about respect. Can you do better? Absolutely, you're always looking to do better. "
Jones, whose father was a police chief and uncle a state police commander in Michigan, said his athletes "don't get away with many things" under the school's strict disciplinary process.
"These isolated incidences are not an indication of what we have, the type of character that we have in our football program, and the culture that we have in our football program," Jones said. "We have good people here. We support each other. The culture that exists here and what's being portrayed are two totally different things."
'Deliberate indifference' cited
In support of its claim of "deliberate indifference" by administrators to sexual assaults at the 27,000-student public university, the complaint includes a string of alleged incidents involving student athletes going back to 1995.
The lawsuit accuses the university of a pattern of "grossly inadequate discipline and resolution in favor of male, 'major sports' athletes."
That favoritism, the complaint said, included "interfering with and stopping the disciplinary process, concealing charges and investigations involving male athletes, arranging for specialized defense counsel for male athletes ... facing criminal and sexual assault charges."
One incident listed as an example in the lawsuit is a 1996 sexual assault complaint against Manning by the university's first female associate trainer, who is not a party to the current case. Manning would go on to lead the Volunteers to an SEC championship one year later.
Manning played at Tennessee from 1994 to 1997.
Manning incident 'a backdrop' to case
The lawsuit is about the university's systemic problems in handling sexual assaults, with mention of the Manning complaint "simply a backdrop to the institutional issues," attorney David Randolph Smith, who represents the accusers, told CNN on Wednesday.
"The issue is how the university is handling sexual assault claims today, but the history has some relevance," said Smith, who added that more accusers are expected to join the lawsuit.
In the Manning complaint, then-trainer Jamie Ann Naughright alleged that the nude quarterback "sat on her face" while she treated him for an injury, according to the Title IX lawsuit. The case was settled in 1997 on the condition that Naughright leave her position, the lawsuit said.
Naughright later sued Manning for defamation after he, in a book, described the alleged assault against her as a "crude, maybe, but harmless" incident in which he "dropped the seat of my pants" and "mooned" another athlete. He said Naughright "had a vulgar mouth" and that allowing women in the locker room was "one of the most misbegotten concessions to equal rights ever made."
Manning wrote: "I admit that even in the context of 'modern' life, what I did to offend this trainer was inappropriate. Not exactly a criminal offense, but out of line."
CNN has been unable to reach Manning's representatives for comment.
'A smear ... plain and simple'
Bill Polian, the former Indianapolis Colts general manager and president who drafted Manning, told ESPN this week
that the lawsuit's brief mention of the old complaint "fits the definition of a smear ... plain and simple." He referred to the accuser as the "so-called or alleged victim."
"It's just a question of a person who's lived a great life, great professional life, contributed to every community he's ever been in, including the University of Tennessee, where a street is named after him," Polian said of Manning. "And it's just an attempt to gain notoriety for others by smearing a good person."
In the five alleged sexual assaults cited in the Title IX lawsuit, only two -- involving prominent former members of the football team -- resulted in criminal charges, said Smith, the accusers' attorney. The men, who are awaiting trial, remained in school. One attended his graduation.
In another alleged assault, involving a basketball player, the man transferred to another university after an administrative proceeding determined there was sufficient evidence that the assault had occurred, according to Smith.
University: Claims 'simply not true'
The lawsuit claims the university's administrative hearing process is "one-sided" and "denies victims the rights to a hearing and to the same equal procedural, hearing, and process rights as given to perpetrators of rape and sexual assault." It also accuses the university of providing lawyers for students accused of misconduct and interfering with investigations.
Those hearing the complaints against students are appointed by the university, which also decides all appeals, according to the lawsuit.
Bill Ramsey, a lawyer for the university, said Tennessee officials "acted lawfully and in good faith" in responding to the incidents mentioned in the complaint.
"We don't arrange lawyers for them; that is not so," Ramsey told CNN in an interview. "That the system or the way it works is skewed to assist athletes is just simply not accurate. The system is fair-minded, fair-handed (and) provides due process to all involved."
In a statement last week, Ramsey said: "Any assertion that we do not take sexual assault seriously enough is simply not true. To claim that we have allowed a culture to exist contrary to our institutional commitment to providing a safe environment for our students or that we do not support those who report sexual assault is just false."
Recent sexual battery allegation not related to lawsuit
Last week, in an incident not related to the Title IX lawsuit, University of Tennessee police said defensive tackle Alexis Johnson was charged with sexual battery, false imprisonment and domestic assault. However, Johnson's attorney and a warrant from the Knox County Sheriff's Office said he faces two counts: aggravated assault and false imprisonment. The alleged assault occurred Sunday at a residence hall.
Gregory Isaacs, who represents Johnson, said his client will plead not guilty at his arraignment next month. "Alexis Johnson has cooperated with every aspect of the investigation," Isaacs said in a statement. "Alexis adamantly denies the allegation. ... Mr. Johnson looks forward to having this matter resolved as expeditiously as possible."
Ryan Robinson, the university's athletics communications director, said in a statement that Johnson "has been suspended from all football activities" but declined further comment.