The San Francisco 49ers are a mess. During Jim Harbaugh’s first three seasons as Niners head coach, his team was 22-0 with a lead of more than seven points at halftime. They’ve now blown such leads in consecutive weeks, having given up a 10-point lead to the Bears in Week 2 before allowing the Cardinals to come back from an eight-point deficit Sunday. The disappointing losses have inspired open revolt from a team that already seemed volatile heading into the season, with Frank Gore openly grumbling about his lack of touches in the second half last week. A topsy-turvy offseason has left the Niners with a lumpy, limited roster, and talents missing via injuries (NaVorro Bowman) or suspensions (Aldon Smith) have exposed major problems. Is it time to panic at Levi’s?

Well, let’s figure out what’s happening to the 49ers after they come back out for the second half before putting their overall performance into historical context. Through the first three weeks of the season, the 49ers have scored 59 points in the first half, more than anybody else in football. In the second half, the Niners have scored — and this is not a typo — three points. As you might expect, that’s far worse than anybody else in the NFL.

First to worst is pretty brutal, but how does that manifest itself in terms of San Francisco’s style of play and output on a per-play basis?

Category First Half Second Half Third-Down Conversions 11-16 (68.8%) 9-20 (45.0%) Rushing Offense 39 for 191 yards (4.9 ypc) 42 for 145 yards (3.5 ypc) Passing Offense 35-50 (70.0%), 395 yards (7.9 YPA), 4 TD, 1 INT 31-44 (70.0%), 299 yards (6.8 YPA), 0 TD, 2 INT Sack Rate 2.0% 10.2%

If you want to pass around the blame for San Francisco’s second-half offensive collapse, more has to go to the rushing offense than the passing attack. This was once the most fearsome rushing attack in football, led by a dominant offensive line. You knew what they were going to do and couldn’t stop them. Now, for a variety of reasons, the 49ers simply haven’t been able to run when they’ve needed to kill clock and move the game along. That was obvious against Arizona last week, when San Francisco’s running backs carried the ball 10 times and gained just 24 yards. Gore finished the game with six carries for 10 yards, which tells you why he didn’t get the football in the second half, especially given that Colin Kaepernick was 25-of-26 for 219 yards on throws to his big three wideouts, Michael Crabtree, Anquan Boldin, and Stevie Johnson.

The decline in the run game, matched with a notable increase in sack rate during the second half, suggests that the offensive line has been a significant portion of San Francisco’s struggles in the final two quarters this year. Some of those sacks are coming from a scrambling, desperate Kaepernick, but the line hasn’t looked great on film this year, either.

That’s mostly come from the right side. Right guard Alex Boone held out all offseason before returning to the team just before camp, and after sitting out for virtually all of the Week 1 win over Dallas, he has been inconsistent during the two-game losing streak. Boone had an ugly whiff in a key moment against Arizona strong safety Tony Jefferson last week, with the twisting Jefferson taking down Kaepernick for a sack that ended San Francisco’s last possession while within seven points in the fourth quarter. Backup right tackle Jonathan Martin, who has filled in for an injured Anthony Davis, was a mess against the Bears.

Left guard Mike Iupati and new center Daniel Kilgore haven’t distinguished themselves, either. The 49ers haven’t gotten much of a push from the line, and that’s a killer for a patient back like Gore, who lacks the top-end speed and acceleration to blow past guys with a cut to the outside. No back in football is better at letting his blocks develop before bursting through the hole than Gore, but the blocks haven’t been anywhere near as reliable in 2014.

Horrible Hour

The problems haven’t been quite as pronounced on defense, but they’ve still been extremely noticeable. Through three weeks, the 49ers have allowed the league’s third-fewest points (16) during the first half, only to give up the fifth-most points (52) during the final two quarters. Are they experiencing the same style issues that the offense is struggling with?

Category First Half Second Half Third-Down Conversions 7-18 (38.9%) 9-13 (69.2%) Rushing Defense 40 for 185 yards (4.6 ypc) 27 for 69 yards (2.6 ypc) Passing Defense 28-51 (54.9%), 246 yards (4.8 YPA), 1 TD, 3 INT 36-53 (67.9%), 455 yards (8.6 YPA), 6 TD, 0 INT Sack Rate 3.8% 3.6%

Not at all. They’re certainly worse on third downs, but teams have been so effective against them on first and second down that third down hasn’t really come up. The Bears, to pick one team, faced only one third down against San Francisco all second half. The rushing defense has actually hunkered down, but the passing defense has totally fallen apart. Basically, once the halftime whistle blows, the San Francisco pass defense has turned opposing quarterbacks from Blaine Gabbert into Aaron Rodgers. That’s the wrong way to live.

At the center of those problems is defensive back Jimmie Ward. It was very surprising to see the 49ers draft Ward with the 30th pick of the first round this spring given what they had done with their personnel earlier in the offseason. The 49ers had lost four key contributors to their secondary, including their starting strong safety (Donte Whitner) and their three top cornerbacks (Carlos Rogers, Tarell Brown, and the retired Eric Wright). Their only signed replacement was former Colts starter Antoine Bethea, who seemed likely to form up with 2013 first-round pick Eric Reid to give the 49ers a strong core at safety. Despite a draft rich in cornerbacks, the 49ers didn’t choose one, instead opting for … another safety.

The 49ers ended up bringing in Ward to play hybrid nickel corner in much the same way that Tyrann Mathieu did for Arizona last year. While the likes of Chris Culliver and Chris Cook have been bad this year, Ward has been the worst member of the 49ers secondary. The television broadcast Sunday credited him with three touchdowns against during the first two weeks, which is bad, and it only got worse. Ward was in coverage on a touchdown pass up the seam to speedy rookie wideout John Brown. It appeared after the catch that there were miscommunication concerns, but given that Ward was the closest player at hand and trailed Brown from the moment the ball was snapped, it seems fair to say he had a lot to do with the coverage on the play. With no pass rush to hide those mistakes, Ward’s been punished for his naïveté this year.

Much of the Arizona game plan from last week was simply targeting Ward and those overmatched cornerbacks. Bruce Arians’s offense is designed around getting the ball downfield for big plays, but Drew Stanton seemed to be tossing bombs on each and every passing play. Against the 49ers, the average Stanton pass attempt (per ESPN Stats & Information) traveled 14.9 yards in the air, a downright staggering figure. Nobody else came close to producing passes that long this week, and it has been a long time since anybody topped him. The last time a quarterback averaged that many yards in the air per pass was in Week 6 of the 2012 season, when Russell Wilson averaged 15.2 air yards per pass attempt in Seattle’s 24-23 victory over New England.

Stanton turned the game around when he started hitting on some of those downfield throws. On passes the NFL defines to be “deep” throws (those that travel 15 yards or more downfield in the air), Stanton went just 1-of-6 for 36 yards in the first half. During the second half, Stanton and his receivers lit up the 49ers. He completed four of his seven deep passes for a total of 114 yards and two touchdowns, with two additional attempts yielding a roughing the passer penalty and a 21-yard defensive pass interference call. Hard to argue with those results.

Pull My Pants Up Tight

So, is it time to freak out about the 49ers? Is there something sinister lurking in their second-half performances that Harbaugh isn’t going to be able to correct? My suspicion is that things will work out just fine, and I think I have a good reason why. Blowing second-half leads is bad, but to get a second-half lead, you have to outplay teams during the first half. And if the 49ers are outplaying teams during the first half, chances are they’re playing better football than their record might indicate. (It also might be worth noting that the opponents they’ve played are a combined 5-1 in their games against non-49ers opposition this year.)

I was curious, so I went back through 1990 and tried to find teams that were similar to the 49ers to see if second-half collapses were a regular problem. During this three-game stretch, the 49ers have had a point differential between halves of minus-92. That’s a little obtuse, so let me put it in table form:

Opp First-Half PD Second-Half PD Diff vs. Cowboys +25 -14 -39 vs. Bears +10 -18 -28 vs. Cardinals +8 -17 -25 Totals +43 -49 -92

That’s saying the 49ers outscored the Cowboys by 25 points in the first half, but were outscored by the Cowboys by 14 points during the second half, with the difference between those two figures representing a 39-point swing. Factor in those figures for all three games and you get a 92-point swing from their first-half point differential to their second-half point differential.

That’s an enormous gap. It’s the fourth-largest differential over any three-game stretch for a team since 1990, a list topped by the 2011 Vikings, which blew halftime leads of 17-7, 17-0, and 20-0 during their first three games of the season and posted a 105-point swing from half to half. Those losses promptly agitated the local media and fan base into calling for Donovan McNabb’s head after a perfectly competent start to the season, and by Week 6, McNabb was out for Christian Ponder, who played worse and got better results. (Probably because he had the It Factor.) They didn’t make the playoffs, but the only other team with a 100-plus-point swing from half to half were the 2007 Chargers, who were the third-best team in a stacked AFC that year and made the AFC Championship Game.

More notably, the second-half woes don’t seem to stick. I went and found the 30 worst three-week stretches in terms of that half-to-half point differential since 1990, a group in which the average team performed 78.3 points worse in the second half than it did in the first half. If those teams were consistently blowing first-half leads, we would expect to see them maintain some level of poor play in the second half over the other 13 games in their schedule. And that’s just absolutely not the case. In the remainder of those schedules, those teams were actually narrowly better (plus-0.4 points) in the second half than they were in the first half.

In other words, there’s little reason to think the 49ers will continue to blow first-half leads. I say that with some trepidation knowing they’re playing the Eagles this week, who have basically been the inverse of the 49ers; they’ve been outscored by 27 points in the first half and produced massive comebacks while outpacing the opposition by 50 points after halftime, a 77-point swing in the opposite direction from San Francisco.

More realistically, the 49ers don’t have the ability to concentrate their successes or failures in any one half. They’re not using up their money plays in the first quarter or running out of gas in the third. Their overall performance is far more important than what they’ve done split by half, and the bigger picture points to a team with notable strengths (the passing game, rush defense) and weaknesses (pass defense, running the football), regardless of how they’re split by time.

Given how successful the 49ers have been over the past few seasons and how well they’re coached, it would be a surprise if things didn’t get better. Boone should play better as he gets back into game shape. Both Anthony Davis and Vernon Davis are on their way back, with the latter likely to suit up in Week 4. Ward will make fewer mistakes (or play fewer snaps). Let’s remember that San Francisco was also 1-2 last year, having suffered blowout losses by 20-plus points in back-to-back games at Seattle and at home against Indianapolis. The 49ers promptly righted the ship, won their next five games, and finished 12-4. Repeating that many wins might be tough, given that there are still two games against Seattle to go and matchups against Denver, Philadelphia, and New Orleans. But it’s too early to panic. The 49ers should be fine.