BATON ROUGE, La. – Most of the fans already had left the stadium. Quarterback Jarrett Lee had been booed and benched in the first half. But somehow, LSU found a way to follow one of its most disheartening losses with the biggest comeback in school history.

LSU rallied from 28 points down to beat Troy, completing the comeback when Charles Scott scored with 4:50 left to put the 19th-ranked Tigers ahead in a 40-31 win Saturday night.

LSU’s biggest comeback at home had been 20 points, when the Tigers rallied from a 34-14 fourth-quarter deficit to beat Houston 35-34 in 1996. Its largest comeback had been from 21 points down at Ole Miss in 1977.

Troy went up 31-3 midway through the third, but LSU (7-3) answered with a touchdown late in the quarter and then ran off 30 points in the fourth to avoid an embarrassing loss.

“We just had to calm down and stay focused,” said Lee, who returned to start the second half. “Not one time did we think we were going to lose. It just shows how much character this team has.”

LSU scored touchdowns on three consecutive possessions to cut Troy’s lead to 31-24 with 10:33 left.

The go-ahead score was set up when a punt bounced off the leg of Troy’s Jorrick Calvin and the Tigers recovered at the Trojans 16. Scott scored four plays later in front of a two-thirds empty Tiger Stadium.

The Tigers led 33-31 after Scott scored and Colt David missed the kick. Quinn Johnson scored his second touchdown with about 2 minutes left to finally put the Trojans at a safe distance.

Levi Brown completed 34 of 72 passes for 312 yards and two TDs for Troy (6-4), which scored touchdowns on its first two possessions and was seeking its second victory against an SEC team. LSU avoided its first loss to a Sun Belt team in 33 games.

The comeback started when true freshman quarterback Jordan Jefferson touched the pylon on a fourth-down bootleg to cut the deficit to 31-10 with 1:26 left in the third quarter. As the Tigers gathered momentum, Brandon LaFell caught a 33-yard touchdown pass at the 14:00 mark of the fourth quarter and Johnson followed with a score from the 1.

LaFell had career highs with 12 receptions and 126 yards. Lee finished with 20 completions in 34 attempts for 216 yards.

“We wanted to build Jarrett’s confidence and we were able to do that,” said wide receiver Terrance Toliver, who had four catches for 54 yards in the second half. “We knew if we could get Jarrett in the groove that we could get going and put points on the board.”

Brown threw for just 26 yards in the fourth quarter. With the Trojans protecting a 31-17 lead, he threw incomplete on fourth-and-1 from the LSU 40 as coach Larry Blakeney gambled to reverse the slide.

“If you do what we do, you have to do it all the time,” Blakeney said. “You can’t do it for a half and then lock down with a wishbone in the second half.”

Brown also had a costly interception that safety Chad Jones returned to the Troy 13, leading to a field goal.

“I was just thinking we could not let this happen for our seniors on homecoming,” Jones said. “We knew we had to go out there and make something happen.”

Nothing in the first half indicated LSU would come back in the second. Troy drove 88 yards on 16 plays for a touchdown the first time it had the ball, then scored another touchdown on its second series.

The Tigers failed to pick up a first down on five consecutive series after David’s 52-yard field goal cut the deficit to 7-3. During that futile stretch, Lee had an interception returned for a touchdown for the seventh time this season, with linebacker Terence Moore returning an easy pick 22 yards for a 24-3 lead.

“I blame me for the way we started that game,” LSU coach Les Miles said. “We didn’t show confidence in our quarterbacks, and we tried to hamstring them. We told them we were going to run the football, and they loaded up the line.”

The game was supposed to be played Sept. 6 before Hurricane Gustav went through Baton Rouge, postponing it more than two months. The Tigers, coming off an overtime loss to Alabama, committed several mental mistakes.

LSU’s offense and defense were penalized once each for illegal substitutions in the first quarter. Trindon Holliday tried to field a bouncing punt, let it slip through his hands and barely recovered the ball before getting swarmed.

The last play of the first half summed up the first 30 minutes. With LSU trailing 24-3, Miles elected to let the clock run down to 3 seconds on fourth-and-1 from the 24 and attempt a 42-yard field goal, but holder Brady Dalfrey dropped the snap.

Fans began leaving the stadium soon afterward, missing a spectacular finish.

“Honestly, we thought we had it in the bag,” Moore said. “But we still had 30 more minutes to play.”