By Morris Phillips

The 49ers tense, lengthy afternoon in the familiar cauldron of the Superdome netted them a desperately-needed win, but left a bunch of questions about the team’s near future.

Somehow, the 49ers survived a near-empty second half and overcame the Saints, 27-24 in overtime.  The 49ers led 14-3 after a quarter, 21-10 at the half, but their offense disappeared in the second half as it has in most of their games this season until a Phil Dawson field goal with a minute remaining got them even.

How poor has the 49ers’ offense been after halftime?  Poor.  In five of their nine games, the team has scored three points twice and been shut out three times.  Both losses at Levi’s Stadium can be easily attributed to the offense disappearing as the Bears roared back to beat the 49ers in Week 2 and the Rams were held to a field goal after the half, but it was enough to break a 10-10 halftime tie last week.

Against the Saints, as the defense battled to keep Drew Brees at bay, the offense ran 20 plays and punted four times after halftime as the 49ers’ double-digit lead disappeared.  In the final drive of regulation, the 49ers didn’t exactly recover, running eight plays, seven of which didn’t gain a yard.  The remaining play of the drive went for 51 yards as Colin Kaepernick scrambled and fired deep to a wide-open Michael Crabtree.  In the ensuing three plays, the 49ers had opportunities to win the game, but Kaepernick threw incomplete each time.

Still the big completion to Crabtree set up Dawson’s game-tying field goal, but the lack of offensive execution left the door open for the Saints with a minute still remaining on the clock.

On the afternoon, Kaepernick did some wonderful things, but for the most part misfired.  The fourth-year quarterback completed less than half his passes, 14 for 32, and was sacked four times.  To be fair, a number of Kaepernick’s passes were dropped, but just as many simply weren’t were they needed to be.

After all the struggles, it only made sense that the 49ers pulled out the game with no help from the offense in overtime.   After all the back and forth, a game that was almost won and surely loss turned on two plays, both pulled off by the defense.

On the final play of regulation, the Saints were limited to a Hail Mary pass near midfield but 6’5” Jimmy Graham emerged from the pack to catch the apparent game-winner.  But Perrish Cox, Graham’s primary defender was pushed by the tall tight end right before the catch.  Normally, the push would go unnoticed but Cox did such a good job of selling the impact of Graham’s fully-extended arm, the referees were forced to make a call.

So as Coach Jim Harbaugh tossed his clipboard in disgust in reaction to Graham’s catch, the 49ers were headed to overtime with a second opportunity.

“When I saw the flag, I said, ‘Thank God,’” Antoine Bethea said.  “I was telling the guys in the locker room if we’d ended the game like that I’d be sick and I wouldn’t sleep all week.”

Saints coach Sean Payton saw it differently saying, “I saw it.  It looked clean.”

In overtime, with half the period exhausted and the possibility of the NFL’s second tie of the season, linebacker Ahmad Brooks came up with the big strip of Brees giving the 49ers the ball at the Saints’ 18-yard line and in position for an immediate, game-winning field goal attempt.  It wasn’t the first, significant meeting of Brooks and Brees with last season’s controversial roughing call on Brooks on many observer’s minds.  This time, the normally sound Brees held the ball too long giving Brooks an opportunity for the strip.

“I was rushing and turning the corner and thinking to myself, ‘Dang, is he going to throw the ball, yet?’  But he didn’t and I was able to make a play,” Brooks recalled.

“It’s kind of poetic justice that he made the play there.  The referees got it right this time,” 49ers’ defensive coordinator Vic Fangio said of the strip and fumble that drew no referee’s flags.

With the win, the 49ers (5-4) avoided falling below .500 with seven games remaining.  Instead, they remain on the fringes of the NFC West hunt looking up at Seattle (6-3) and first-place Arizona (8-1).  But even a must-have win can’t mask the fact that an offense missing only starting center Daniel Kilgore has struggled for most of the season.

Meanwhile, the 49ers’ defense fell prey to the injury bug again as defensive lineman Ian Williams suffered a leg injury and did not return.  Patrick Willis missed a third straight game due to a toe injury amid reports he could miss significant time due to a sluggish recovery from that injury.  In Willis’ place, rookie Chris Borland has been fantastic, registering double-digit tackles for the second straight game.

The win ended the Saints’ 11-game home winning streak dating back to December 2012.  Despite the loss the Saints still hold first place in the NFC South at 4-5.  If New Orleans goes on to win the division, the possibility looms that they could host the 49ers in a wild card weekend matchup that would be the fourth in the last three seasons between the two clubs in New Orleans.

The 49ers welcome back Aldon Smith next week in New York when they face the Giants and are hopeful that they will get Glenn Dorsey, NaVorro Bowman and Willis back in the coming weeks.