But O'Brien persevered in a way that drew national praise for a program that had been blasted for months. Aided by a devoted group of seniors, he kept the team together. He urged his players not to feel sorry for themselves. He recommended that fans and the Penn State community look ahead and unite.
And he showed, in his first year ever as a head coach, that he could do the job. The Nittany Lions won eight of their last 10 games to finish 8-4. Their season-ending overtime win over Wisconsin, which would later play in its third straight Rose Bowl, was one of the most dramatic games in the history of Beaver Stadium and sent the Lions and their fans into the offseason on a cheerful note.
The seniors are gone, including the inspirational Michael Mauti and record-setting quarterback Matt McGloin. Now the 43-year-old head coach builds another team with another group of worthy senior leaders but questions at quarterback, where the starter for Saturday's season opener against Syracuse will be taking his first snap in a major-college game.
Less than a year after winning a plethora of coach of the year awards, O'Brien said he'll do a better job this season, and that both the offense and defense will be different than what was seen in 2012.
"I know the players a lot better," he said. "I learned a lot about organization and how important it is to just basically state your philosophy, your goals, just about every day or every time you have a staff meeting. I've learned to communicate better, too."
The biggest decision of the preseason has yet to be made. Sophomore Tyler Ferguson and true freshman Christian Hackenberg have been battling throughout camp for the right to be Saturday's starting quarterback. Ferguson has the benefit of a year in junior college and a full spring practice with Penn State, while Hackenberg has learned quickly since arriving on campus in June.
O'Brien has called the pair "the two best young quarterbacks I've ever coached" and indicated the reason that he's taken so long to choose one is because "I want to keep getting these guys a lot of reps and make sure that they see a lot of different looks and get to throw the ball to all the different receivers equally."
Whoever gets the job will have no shortage of support. The Nittany Lions' skill players are led by junior Allen Robinson, the Big Ten's only 1,000-yard wide receiver last year, and junior Zach Zwinak, who rushed for 1,000 yards. The offensive line is a veteran unit led by all-Big Ten guard John Urschel, one of the senior leaders.
"It comes with getting a little older, getting a little more experience, being more comfortable in your role as a player," said Urschel, a 4.0-grade-point-average student who will study for a second master's degree this year. "That's a role I've embraced, and I'll do all I can to help my football team, whatever that may be."
The Lions also have four tight ends who will be in a variety of formations designed by O'Brien, plays culled from his years as offensive coordinator of the New England Patriots. The position is led by all-Big Ten performer Kyle Carter.
The Penn State defense will see some new looks under John Butler, a La Salle High School product who will serve as a major-college defensive coordinator for the first time. Because of depth issues at linebacker, there may be some packages where a safety moves into a linebacker position.
"He's done an excellent job," O'Brien said. "He's one of the best coaches I've ever been around. He's tough. He's a great communicator. The kids really respect him. We have a competitive practice because he and I are competitive people."
The Lions seem to have one of everything in the front seven - a fine pass rusher in end Deion Barnes (Northeast High), a tough run-stopper in 318-pound tackle DaQuan Jones, a fierce hitter in middle linebacker Glenn Carson, and a quick sideline-to-sideline talent in outside linebacker Mike Hull.
O'Brien and Butler beefed up the secondary by moving two wide receivers over to the defensive backfield. One of them, Trevor Williams, should start at the corner. Penn State also is deep at safety, led by versatile junior Adrian Amos.
Junior Sam Ficken, who got off to a horrendous start last season, takes a streak of 10 successful field-goal attempts into 2013. The Nittany Lions ranked at or near the bottom of the Big Ten in many punt and kickoff categories, and O'Brien promises improvement in those areas.
The Nittany Lions have four opponents that are considered Big Ten title contenders. Two are at Beaver Stadium (Michigan, Nebraska), and two are away (Ohio State, Wisconsin). There is some consensus that they can match their 2012 total of eight wins, but they have to stay relatively free of injury, and one quarterback must step up.
A look at the Nittany Lions
Head coach: Bill O'Brien (second season, 8-4).
Last season: 8-4 overall, 6-2 Big Ten, second in Leaders Division).
Top returning starters: WR Allen Robinson, DE Deion Barnes, G John Urschel, DT DaQuan Jones, TE Kyle Carter, RB Zach Zwinak, S Adrian Amos, LB Mike Hull.
Top newcomers: QB Christian Hackenberg, RB Akeel Lynch, LB Nyeem Wartman, CB Trevor Williams, WR Eugene Lewis, TE Adam Breneman.
Ferguson vs. Hackenberg
The preseason has been dominated by the starting-quarterback competition between sophomore Tyler Ferguson and freshman Christian Hackenberg. The 6-foot-3, 213-pound Ferguson, who played one season at the College of the Sequoias in California, benefited from his time in spring practice with the Nittany Lions. Hackenberg, 6-4 and 220, didn't arrive on campus until June but has shown why he was one of the nation's top high school quarterbacks last season. Head coach Bill O'Brien, behind on his previously stated timetable as to when he would announce his decision publicly, said the starter will get most of the snaps in a game but the No. 2 man will play some.
A concern for the Nittany Lions in training camp, and for the foreseeable future, is depth. Even though NCAA sanctions don't require them to reduce their number of scholarship players to 65 until the 2014 season, the Lions began camp with fewer than 70. Because of the low numbers, O'Brien decided to cut down on live tackling in the preseason, choosing to go with the "thud" method _ hit the ballcarrier, then release him. This might prove to be a disadvantage to Penn State's skill players when hostile opponents start hitting them, but it's doubtful the defense is affected.
Still Linebacker U., but ...
Depth issues have affected the Lions' linebacking corps. While they have three excellent starters in Glenn Carson, Mike Hull, and Nyeem Wartman, the numbers behind them are thin. O'Brien said only a total of "five or six" linebackers are prepared to play in the season opener although he hopes to build more depth as the season goes on.
Duck! Here comes Barnes
Deion Barnes, the former Northeast High star, is expecting to have a better year than in 2012, when the Big Ten named him its freshman of the year. Barnes, who showed his playmaking ability with six sacks and three forced fumbles last season, said more experience and more film study will allow him to play the run better this year. If he can show the coaches that ability, he will be on the field for more plays and potentially become a force for the entire game.
Contact Joe Juliano at email@example.com. Follow on Twitter @JoeJulesInq.