Howard quarterback Greg McGhee was the MEAC rookie of the year last season, but was forced to begin this year with an NCAA-mandated three-game suspension. (John McDonnell/The Washington Post)

As the Howard University football team’s Sept. 1 season opener against Morehouse crept closer, sophomore quarterback Greg McGhee went through practices, position meetings and film sessions as usual.

But instead of preparing for his 12th career start, McGhee was about to watch the Bison from the sideline for the first time. “Keep your head up,” he heard more than once before his three-game, NCAA-mandated withholding began. “Those three weeks will come and go faster than you know.”

At the time, McGhee — the 2011 Mid-Eastern Athletic Conference rookie of the year — wanted to believe them. Almost two months later, the quarterback still appreciates the sentiment, but now it also draws a slight chuckle.

“It was actually the longest four weeks ever because we had the bye in there, too,” McGhee said.

After a breakout campaign last fall, McGhee figured to enter this season as one of the most important pieces in Coach Gary Harrell’s rebuilding project at his alma mater. Instead, McGhee was one of 11 Howard football players who missed time as a result of an NCAA investigation into their improper use of textbook allowances.

The Bison (4-2, 3-1) battled through the stretch and won four of their first five games in their best start in nearly two decades, allowing McGhee to return to a team near the top of the MEAC standings. Heading into Saturday’s homecoming game against Morgan State (3-3, 2-1) at Greene Stadium, McGhee is grateful to be starting again after getting a lesson in perspective.

“Mistakes happen, but for every mistake, there’s a consequence,” said offensive coordinator Ted White, a decorated Howard quarterback in the late 1990s. “He was pretty much a grown man about the situation. He learned from it, and I know he won’t let anything like that happen again.”

The other two quarterbacks on the roster — junior Randy Liggins Jr. and freshman Jamie Cunningham — each had the chance to start in McGhee’s stead, and Howard’s lack of quarterback depth actually worked in the team’s favor.

The NCAA allowed McGhee to dress and warm up for each game, in case of emergency. The 6-foot-3, 200-pounder from Pittsburgh continued to practice with the team and pore over the quarterback study guide that White prepares for each opponent.

Against Morehouse and Rutgers to start the season, McGhee stayed on the sideline with a headset on, counseling his backups between series. But Cunningham didn’t dress at Norfolk State on Sept. 15 because of an ankle injury and McGhee was forced into action late in the first quarter when Liggins went down with back spasms.

McGhee ran for Howard’s final touchdown in a 37-36 overtime victory against the reigning conference champion. Harrell said the NCAA also allowed senior running back Terrence Leffall — the team’s leading rusher last season — to stagger his three-game withholding to play in that game. Both players finished serving their punishments the next week in a blowout win over Savannah State.

“It was stressing,” McGhee said of his time on the sideline. “I wouldn’t say [I was] depressed, but it was very hard to take. I’d never had to watch my team play without me and I wanted to help out my teammates.”

In two starts, McGhee has struggled to return to last year’s form. He’s thrown just one touchdown and four interceptions, two of which were returned for touchdowns in last Saturday’s 38-10 loss at North Carolina A&T.

Harrell said McGhee has continued to make the simple mistakes — not taking enough time on his pre-snap reads, not sticking with his progressions and sloppy footwork — that he worked hard to eliminate last season.

Still, the second-year coach said the quarterback’s handling of a difficult situation this season has only enhanced the staff’s opinion of him. It’s no coincidence McGhee was handed the No. 7 jersey — once worn at Howard by White and former NFL quarterback Jay Walker — when he arrived on campus.

“We’ve got a guy that we feel like we can make the face of the program,” Harrell said. “Looking at the history of Howard University, we were always successful when we had a quarterback that could lead us in the right direction.”