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Why can’t the Niners hold a lead?

They usually start strong anyway, but that’s not enough.

NFL: New York Giants at San Francisco 49ers Kirby Lee-USA TODAY Sports

14-0 and 17-6 over the Los Angeles Chargers.

30-23 over the Green Bay Packers.

15-3 over the Arizona Cardinals.

20-10 over the New York Giants.

This edition of the San Francisco 49ers can build a lead over a lot of teams, some of them actually good, but it has a terrible time holding on to those leads. What’s going on? Why can’t they close out games?

What makes this even more frustrating is that, with starting QB Jimmy Garoppolo out injured for the year, this team has developed a really strong running game behind a powerful, rebuilt offensive line and the emergence of Matt Breida and Raheem Mostert as effective second- and third-option running backs.

This is a team whose offense works naturally at a four-minute drive pace, even in the first half. It’s actually how they build those leads in the first place, punctuated by catch and run plays to TE George Kittle and FB Kyle Juszczyk. This is a team tailor-made to hold on to leads. And yet they can’t.

It’s tempting to draw grand conclusions about Kyle Shanahan as a coach, given the FalconsSuper Bowl collapse against New England in the recent past, when he was their OC. But Shanahan had no role in Atlanta’s defense, and a team can’t come back like that without scoring lots of points — even if they’re not as dominant as the Patriots. So I don’t think that Super Bowl is a legitimate piece of evidence one way or the other.

But the defense IS under his watch now. So is it the defense, the offense, or a combination of both? Is Shanahan a great opening script writer, who gets out-maneuvered with halftime adjustments? A great offensive coach who either neglects his D, or is saddled with a bad defensive coordinator? Or something else altogether?

Let’s look at the details of these four lost leads this year and see what patterns emerge.

We’ll start by acknowledging some realities. The 49ers are not a good team this year, especially with their starting running back Jerick McKinnon, starting quarterback Jimmy Garoppolo, and starting free safety Adrian Colbert on injured reserve. Hopes for this year were based on projecting a lot of success from late round picks (such as Colbert), UDFAs (RB Matt Breida and rando under-the-radar acquisitions (DL Cassius Marsh, WR Kendrick Bourne). In other words, they were always kind of unrealistic. That said:

1) Week 4 @ LA Chargers, 29-27 loss

This was on the road, in the first game after Garoppolo was lost for the year with an ACL injury. Los Angeles was not highly regarded at the time, but has proven to be one of the best teams in the NFL this year. So it’s amazing that San Francisco did as well as they did behind QB C.J. Beathard.

The Nines racked up a quick 14-0 first quarter lead behind a pick-six by DB Antone Exum, Jr. and a quick drive (6 plays, 56 yards) that was probably best credited to Kyle Shanahan’s planning. Frankly, they sputtered after that, scoring a TD on one 82-yard pass play to Kittle at the end of the third, and a field goal that capped a 9-play, 49-yard drive.

Meanwhile, the Chargers steadily came back, and got a couple of breaks. A 56-yard punt return earned them a field goal to tie, as the first half ended. Before that, the Niners’ red zone weakness had forced them to settle for a FG after first and goal at the 8. LT Joe Staley was injured in the 2nd quarter, hampering SF’s offense. And in the second half, Beathard — who had an excellent game in general — threw two interceptions.

The teams traded field goals, and the lead, in the fourth quarter, but that second INT sealed the home win for LA.

Bottom line: Against a very good team, on the road, behind a backup QB, the Niners played a very good team tough to the end. No shame here for anyone.

2) Week 6, @ Green Bay, 33-30 loss

Say you had just moved to the U.S. from Mongolia, and were looking at Green Bay’s record as a non-football fan. “Hmm, 4-5-1, I guess they’re not that good.” What you wouldn’t understand would be the significance of QB Aaron Rodgers’ early season injury.

The game against San Francisco was the first game since Week 1 where he wasn’t listed on the final injury report. And the future Hall-of-Famer responded with 425 yards and 2 TDs on 25/46 passing, with no interceptions. Other stuff happened — two long touchdowns to Marquise Goodwin, a highly questionable illegal contact call on Richard Sherman, no takeaways for the 49ers defense, and most importantly, an interception by Beathard with SF perfectly primed for the winning FG, on 3rd-and-3 at the Packers 46 with 1:13 left.

But the bottom line was, on the road with your backup QB against Aaron Rodgers. The Niners almost won, and that — rather than Rodgers driving for the winning FG — was the amazing development.

Bottom line: Aaron Rodgers vs. C.J. Beathard

3) Week 8, @ Arizona, 18-15 loss

This game sucked. Playing a very bad team with a shaky rookie QB, a rookie coach and possibly the least experienced OC in NFL history, that they had seen just three weeks earlier.

Offense? Defense? Both sucked. The Niners managed only one touchdown, and 15 points, against a bad team. The defense gave up two fourth-quarter touchdowns and a 2-pt conversion to a terrible team. The score was 2-0 on a safety SF forced, then 3-2, then 5-3. It was that kind of a game. The game ended on a fumbled snap that blew a reasonable chance at a comeback.

I have no analysis, no insights about this game. It just makes me angry to think about it. I will say that it was the game that convinced me that Beathard was not going to work out. I realize that he got injured, but even if he hadn’t, it still would have been time to bring Nick Mullens in.

Beathard just does not move fast enough to make it in the NFL. Maybe his famous “toughness” has resulted in him taking too many hits, I don’t know. But as I wrote earlier in the season, he always seems like he just woke up from a nap and is moving half-speed. After a couple of games for DC’s to get videotape on him, that’s just not going to work out.

Bottom line: Doom, despair, and turnovers.

4) Week 10, vs. NY Giants 27-23 loss

It’s true that the Niners led this game by 10 points midway through the third period, but that’s misleading. This was a neck-and-neck game between two very bad teams; the lead (or tie) changed eight times during the game. That ten-point margin, the largest of the game, lasted for a total of one minute and 33 seconds.

The mystery of the Giants, for me, is that they have (arguably) the best wide receiver and best running back in the league, and are still so terrible. The reason, of course, is QB Eli Manning (as well as a bad front office that chose not to replace him).

This loss was a team effort. The offense managed only a field goal after taking that 10-point lead, with 6:51 left in the third. This is the one game where I think Shanahan can be fairly criticized for clock management at the end of the game. He called a drive, starting with 8:57 left in the game, that was neither fast enough to set up two score, or slow enough to build to a game-winning field goal.

Instead, the Niners drove 54 yards in six minutes and 11 seconds, leaving a veteran QB who had two great weapons a generous two minutes and 46 seconds to orchestrate a winning drive. (The 49ers injury-depleted secondary made that a very bad scenario.) Ultra-cautious play calling on his final series, with started at the New York 19 with 3:46 left, cost Shanahan the game.

The defense failed to get any pressure, after a couple of good pass rushing games. And the Niners showed the predictable results of having a 3rd-string UDFA QB that their opponent had film on.

Bottom line: A clear failure for both Shanahan and DC Robert Saleh

So that’s what I see. What’s your take on why the 49ers have so much trouble putting games away?