The 49ers’ 2-4 start falls squarely on Kyle Shanahan’s shoulders. Here’s what to do

It’s been a bad, bad six games for San Francisco 49ers coach Kyle Shanahan.

The 49ers are suddenly 2-4 to start 2021, losers of four straight, without the excuses of injuries they could credibly use last year, or a lack of continuity, or a new coach growing on the job.

No, San Francisco is in the fifth season of Shanahan’s tenure. He and his team came in with high expectations — perhaps expectations of getting back to a Super Bowl or at least getting into the playoffs — and now they’re left searching for answers following a dismal 30-18 loss to the Indianapolis Colts, who came to Levi’s Stadium sporting a 2-4 record.

Does Shanahan deserve scrutiny?

“Yeah, you lose four games in a row, I’m the head coach of this team. I expect it and I deserve it,” Shanahan said after Sunday night’s rain-soaked game in front of a national audience on NBC.

Poor choices leave 49ers in a hole

There have been a host of decisions gone awry for Shanahan and general manager John Lynch that have gotten them to this point. Some of it is bad circumstance or a product of simple hindsight. But much of it is their own doing.

Namely, their quarterback situation is season-defining contradiction, which is bleeding into their ability to win games.

Shanahan has said Jimmy Garoppolo gives the team its best chance to win. Fair enough.

But it comes on the heels of investing three first-round draft picks, and a 2022 third-rounder, in Trey Lance to be Garoppolo’s replacement. So Shanahan’s rationale is Lance is good enough to replace Garoppolo, eventually, just not yet. All the while Lance has spent the season as the backup quarterback — which means not getting much-needed practice reps to develop — while Garoppolo’s sputtering on the field has played a significant role in the team’s losing.

And when Lance did play, Shanahan clearly didn’t have enough trust in him to run a normal version of the offense. That was evident by the reliance on Lance’s legs. He led the team with 16 carries (nine designed runs, seven scrambles) for 89 yards in his lone start in Arizona, which came because of Garoppolo’s calf injury.

Lance came out of the game with a sprained knee, which prevented him from practicing or working out last week and during the bye, or even being available Sunday night while Garoppolo was returning from his calf injury, which he said he continued to feel during the Colts game.

“I definitely felt it at times. But it sort of is what it is,” Garoppolo said of his calf. “I think all the guys out there, we’re all playing with something right now.”

Having Lance would at least have been an option for Shanahan while the offense went 1-of-11 on third down. But he was hurt.

So Shanahan’s reluctance to give Lance practice reps led to Lance’s run-centric game plan, which would logically lend to a quarterback needing some time in the training room given the hits he was subject to in Arizona. The game plan wasn’t to let running backs carry the load and help Lance; it was to make Lance the centerpiece of the running game. That’s an odd way to integrate the future face of the franchise who will have to win with his right arm. And if he can’t win throwing, that falls squarely on Shanahan, the offensive mastermind charged with his grooming.

Trey Lance needs reps

The only way for Lance to develop is by getting the reps, either in games or practice, but Shanahan hasn’t given him the opportunity after playing just one game in 2020 after one full season as the starter for North Dakota State in 2019.

Now the 49ers will spend the week preparing for their trip to play the Chicago Bears, coming off a game where Garoppolo turned the ball over three times (it could have been four) while the offense had just two first downs over a seven-possession span in the second and third quarters.

“I think we struggled to throw and catch,” Shanahan said.

Garoppolo played poorly against the Colts. His stat line 16 of 27 completions for 181 yards with a touchdown and two interceptions doesn’t tell the story. The three-play touchdown drive early in the fourth quarter was the only time in the game the 49ers pushed the ball downfield, while the Colts and quarterback Carson Wentz were making deep throws throughout the game to great effect, with Wentz either hitting Michael Pittman for big gains or drawing pass interference penalties.

The 49ers were penalized three times for DPI, which all came just before Indianapolis’ three scores (among the list of self-inflicted wounds, Lynch and Shanahan going into the season with Jason Verrett and Emmanuel Moseley as their top cornerbacks has proven to be near the top of the list).

That aside, Shanahan finds himself approaching a crossroads at quarterback, which also depends on Lance’s health. At 2-4, it’s hard to justify playing Garoppolo with Lance so badly needing experience to hit the ground running in 2022, when Garoppolo will likely no longer be on the team. But if Lance can’t play, he’ll have to stick with Garoppolo while it’s evident he’s not trending toward be part of the solution, particularly with his calf injury not entirely healed.

“I have got a whole team to worry about,” Shanahan said. “I’m not just thinking about the quarterback situation right now. I’ll evaluate everything, see where our team’s at, see who gives us the best chance to beat Chicago and see what our options are. You go into each week to find out your options. We had two quarterbacks who were hurting this week. Jimmy was able to come back and play and we’ll see if Trey can next week. Still not sure yet. But we’ve got a lot of things to figure out.”

There were other roster-building mistakes on display Sunday night against the Colts. Such as:

▪ The DeForest Buckner trade hasn’t gone well. Javon Kinlaw, who was added with the draft pick received in the trade, reportedly was flagged by multiple teams ahead of the 2020 draft for knee issues. Shanahan said Friday he’s a candidate to go on injured reserve after battling a knee condition since training camp, which came after needing at least one knee surgery following his rookie season.

Arik Armstead, signed with the money the team saved by not paying Buckner, had four tackles and a tackle for loss Sunday, but didn’t register a sack or quarterback hit. Armstead has 4.5 sacks since Buckner was traded. Buckner has 12.5 since being dealt, including one to end Sunday night’s game, and was an All-Pro in 2020. Armstead said he wasn’t happy with the way he played last year.

Left tackle Joe Staley had a telling take on the Buckner trade during his pregame appearance for NBC Sports Bay Area.

“The leadership that he does, every single day in the locker room, showing guys how it’s done. He’s a true pro, and I think that culture leadership that he brings is missed right now,” Staley said.

Said Buckner postgame: “It was definitely personal for me. I wasn’t trying to get too high or too low throughout the week, but it meant a lot. ... Life went full circle, I like to say. This will be a great plane ride back, for sure.”

▪ Brandon Aiyuk had one catch for six yards and a run for three yards, continuing a disastrous start to his second season. The 2020 first-round pick looked like a potential star as a rookie, leading the team with 60 catches for 748 yards. This season: nine catches for 96 yards in six games. And he nearly muffed a punt for a safety on Sunday night.

Pittman, meanwhile, had four catches for 105 yards and a touchdown, and was Wentz’s target on multiple plays that resulted in pass interference penalties. Pittman has 35 catches 508 yards and two touchdowns this season. He was taken nine spots after the 49ers traded up to draft Aiyuk.

That’s not to say that the team should have drafted Pittman and not Aiyuk. It’s just doesn’t reflect well on Shanahan and Lynch’s process that Pittman is performing at a higher level while Aiyuk is struggling to get targeted.

▪ The number of offensive snaps played for second-round pick Aaron Banks, a guard who was in uniform for the first time in his career: 0. That matches the number of offensive snaps for third-round pick Trey Sermon, the running back from Ohio State.

For a team that needs help at key positions, getting nothing from recent draft picks doesn’t bode well. And it’s putting pressure on those guys to be regular starters in not-too-distant future if they’re going to avoid being considered failed draft picks. The team’s best draftees — George Kittle, Fred Warner, Nick Bosa, Deebo Samuel — were all good enough to have big roles as rookies.

At 2-4, losers of four straight, the 49ers find themselves in a deep hole. It’s a team that’s not living up to its own expectations and should be better given its a group that isn’t too far removed from a Super Bowl appearance.

“We’re way better,” said Samuel, “than our record is showing.”