However, O'Brien refused to allow his players and coaches to feel sorry for themselves and kept his focus on the present while trying to keep his team together. Halfway through his first season as a head football coach, he has led the Nittany Lions to four straight wins after an 0-2 start and attracted national attention.
"To me, it's the story of the year right now in college football," said Kirk Herbstreit, college football analyst for ESPN.
"For Penn State to deal with what they dealt with the entire offseason, it was like a storm cloud that would not go away. For a guy who's never been a head coach to have to somehow think of some way how to navigate through that and then be able to get his team ready to play . . . you can't even put into words the job that he's done and the way he's gone about it."
The story is being directed by O'Brien, 42, a native of Andover, Mass., who is in his 20th year of coaching at the college and pro levels. He has displayed a personality of one who is very attentive to detail, meticulous in his preparation, and serious about his craft - but still having fun with his players.
And yes, there is a fiery personality - which was the only thing his players and the general public knew about him before he arrived in Happy Valley for the first time.
"I really didn't know too much about him other than the time he was yelling at [Patriots quarterback] Tom Brady. That's the only highlight they seemed to show," said defensive tackle Jordan Hill, referring to the video of O'Brien's sideline spat with Brady during a 2011 game.
O'Brien hasn't been afraid to show that passionate side of himself in his new job. After he went on the field on Saturday to check on an injured player, O'Brien yelled at a nearby official, objecting to a pass-interference call against Penn State one play earlier.
The Nittany Lions came back from 11 points behind in that game and defeated 24th-ranked Northwestern, 39-28. They entered their bye week with a 2-0 record in the Big Ten Conference.
"I think he has exceeded everyone's expectations," said Gerry DiNardo, a former college head coach who is an analyst for the Big Ten Network. "Penn State's not the best place in the world to learn how to be a head coach. It's just hard to make mistakes and survive, especially on your first job. But he's made a lot more right moves than a lot of rookie head coaches. He's found a way."
O'Brien challenged the members of his senior class to excel as leaders and loves what they have done. He already has started counting down the games until the time they no longer take the field for Penn State.
The seniors helped O'Brien convince players to stay following the sanctions handed down by the NCAA on July 23. One sanction was that a player could transfer to another Football Bowl Subdivision (formerly Division I-A) school without sitting out a season, a condition that will continue until the start of Penn State's 2013 preseason practice in early August.
While other football coaches were immersed in preparations for their first preseason practices, O'Brien had the added duty of re-recruiting many of his own players. Ten players transferred, including three starters, in the days after the sanctions.
Now Penn State is receiving respect and recognition. Some pundits, including Herbstreit, have tabbed O'Brien as deserving votes for Big Ten coach of the year. Others are boosting him for national coach of the year.
But O'Brien, whose attention rarely strays outside his program, isn't listening to the praise and is fixed on the second half of the schedule starting on Oct. 20 at Iowa.
"We definitely appreciate the respect that people have shown our program," he said. "But it's just halftime. In reality we haven't done anything yet."
Still, the Lions have done more than many had expected.
"I think it's one of the great stories of the season so far," DiNardo said. "I think it's extraordinary."
Contact Joe Juliano at 215-854-4494 or firstname.lastname@example.org, or follow on Twitter @joejulesinq.