Heading into the Week 9 bye last season, the San Francisco 49ers were skidding. Their offense had scored 17 points in each of three consecutive games — all losses — and something felt off. The euphoria of drubbing the Dallas Cowboys 42-10 was long gone, and some anxiety started to set in. The run defense had been flat for several games, quarterback Brock Purdy was committing ugly turnovers and there was a lack of continuity across the board.

The focus at that time was on defensive coordinator Steve Wilks. And Shanahan’s answer to that was moving him down from the booth to the sideline, so he could be in better communication with his players. The next game out, the 49ers held the Jacksonville Jaguars to three points. It was the first of six consecutive 49er victories and San Francisco closed out the season 7-2 before sweeping into the Super Bowl.

It’s a memory that has differing vantages. Some might see it as Shanahan scapegoating his defensive coordinator — who he later fired after a Super Bowl loss to the Kansas City Chiefs — at a time when Shanahan’s own offense was a big part of the problem. Others might see it as Shanahan shaking up his staff’s routine and trying to engage a different dynamic and spark the team.

Whatever it was, it feels relevant to the 2024 iteration of the 49ers. They’re off-kilter again, this time fumbling in a fairly critical 20-17 home loss to the Seattle Seahawks that drops San Francisco to 5-5 and the bottom of an extremely tight NFC West, thanks to a woeful 1-3 record in the division. Sunday’s defeat stung in multiple ways, from star edge rusher Nick Bosa suffering his second oblique injury of the season, to Purdy misfiring under pressure on a key third-down hot read (which could have iced a win for San Francisco), to the 49ers’ defense looking half-asleep as the Seahawks put together an astonishing 12-play, 80-yard touchdown drive in the final minutes of the fourth quarter.

With that drive, the Seahawks put themselves back into the race to win the NFC West — which could produce only one playoff team — and deal a crucial blow to the 49ers’ efforts to move to the top of the division. The complication for San Francisco this year? There is no Wilks to blame. There is no bye week to get things right. And now the focus is starting to shift to Shanahan’s offensive play-calling. This is coming on the heels of a testy tone he took with a 49ers beat reporter on Friday, following a question about the number of plays Purdy has available when he steps to the line of scrimmage.

Oh, and lest we forget, the 49ers’ next two games are both on the road and across the country — first against the 7-3 Green Bay Packers next Sunday, then facing the 9-2 flexing-their-muscles Buffalo Bills in the Sunday night prime-time slot on Dec. 1. That should be a fairly white-knuckling horizon for a San Francisco franchise that is 3-3 in its past six games, has seen Purdy throw six interceptions in that span and is suddenly in the midst of streamlining the offense back through running back Christian McCaffrey, who has played his first two games of the season the past two weeks.

Take a step back, and what you see is a 49ers season that may hang on the outcome of the next two weeks. That’s something San Francisco’s coaching staff had to know hosting Seattle. For a mid-November game, it was a must-win situation — if only to keep the 49ers from giving life to virtually the entire NFC West and ratcheting up the pressure to steal games in very difficult places to win the next two weeks.

“Just extremely disappointed,” Shanahan said of Sunday’s loss. “I thought we had a chance to put them away a number of times throughout the game. I thought the penalties we had on a number of drives just killed us. I thought we had some good momentum and then had a penalty that kind of ended the drive on two big drives — that cost us points on both of them. We still should have put it away there on that last drive and had every opportunity to, and missed a couple opportunities to do that. … When you let people hang around, that’s what happens.”

For Shanahan — who has occasionally (or often) been criticized for his struggles to win tight games late in the fourth quarter — it’s going to only intensify a microscope on his game management. While he’s not calling plays for the defense, it still reflects on the head coach when his team can’t close out close games. Especially when those games are instead seized by an opposing offense and quarterback late. Aside from the Seahawks’ Geno Smith, the 49ers have also given up crucial drives to Matthew Stafford and the Los Angeles Rams and Kyler Murray and the Arizona Cardinals in two losses earlier this season.

It’s not that the 49ers don’t have an ability to win. It’s that they too often don’t have the ability to close. And losing close games makes the margin for error only slimmer in the face of the injuries the 49ers are juggling, including the loss of wideout Brandon Aiyuk for the season, the in-and-out health of tight end George Kittle, the always tense medical status of Deebo Samuel Sr. and McCaffrey, and now the oblique issues with Bosa.

All of that is now weighing on what Shanahan has described as the “second-half surge” that good teams have to put together in NFL schedules. A surge that he isn’t ready to evaluate right now, despite entering a critical point of the season.

“I’m not going to talk about the whole second half [of the season] — the second half of the season just started,” Shanahan said Sunday. “We won last week and lost this week. And I thought we had every opportunity to win this game and we didn’t get it done. We’ve got to make sure we find a way to win next week.”

For now, the 49ers are what they are: The NFC’s defending champions who lost in the Super Bowl and have tumbled to a mediocre 5-5 record. Now they’re heading to the part of the season that could define their 2024 destiny and shape the conversation about who is most responsible. Last year, it was pinned on defensive coordinator Steve Wilks. This year, it’s going to be more difficult for Shanahan to pin the fall elsewhere.