After leading the 49ers to the NFC title game three times and the Super Bowl once in his first three years, Jim Harbaugh saw his reign in San Francisco end with a tumultuous, dysfunctional 8–8 season. Harbaugh says he was pushed out by 49ers owner Jed York and general manager Trent Baalke. The team claims there was a “mutual” decision to part ways. The bottom line is the 49ers lost a coach who went 49–22–1 (including the postseason) and replaced him with Jim Tomsula, their longtime defensive line coach. Tomsula’s only experience as a head coach came during one season in the defunct NFL Europe and the 49ers’ final game in 2010 after they fired Mike Singletary.
“Jim did a heck of a job,” Baalke says of Harbaugh, who took the job as Michigan’s coach. “I think he’s gone his direction, we’ve gone ours. I feel very good about the direction we’re headed, and I’m sure he does as well.”
Defensive coordinator Vic Fangio, the architect of San Francisco’s elite defense, left to fill the same position with the Chicago Bears after being bypassed for the 49ers’ top job. The 49ers promoted offensive assistant coach Eric Mangini, a former NFL head coach and defensive coordinator, to replace Fangio. Offensive coordinator Greg Roman left for the same job with the Buffalo Bills after taking much of the blame for the 49ers’ offensive futility in 2015. Quarterbacks coach Geep Chryst was promoted to replace Roman. Chryst’s only experience as an offensive coordinator was in 1999-2000 for the Chargers under Mike Riley.
Tomsula will try to resurrect a 49ers team that lost a long list of key players, including running back Frank Gore, guard Mike Iupati and linebacker Patrick Willis.
The 49ers believe Harbaugh and Roman strayed too far from the power-running attack last season in an attempt to boost their anemic passing game. Quarterback Colin Kaepernick actually regressed, and the 49ers ranked a dismal 25th in scoring at 19.1 points per game, down from 11th (25.4) in 2013. Kaepernick’s passer rating dropped from 91.6 in 2013 to 86.4 last year, and the 49ers ranked 30th in passing offense, exactly where they ranked in 2013. For the first time in Harbaugh’s four seasons, the 49ers had more passing attempts (487) than runs (470). Even so, the 49ers ranked fourth in the league in rushing at 136.0 yards per game.
As Chryst tries to get the 49ers’ offense untracked, he won’t have Gore, the franchise’s all-time leading rusher, to lean on. Gore signed with Indianapolis as a free agent after the 49ers showed little interest in keeping him. Carlos Hyde, who rushed for 333 yards and four touchdowns on 83 carries in a solid rookie season, will start and should get most of the carries. But he’ll share the running load with veteran Reggie Bush, a key free-agent pickup, and Kendall Hunter, who’s returning from a knee injury.
The 49ers lost wide receiver Michael Crabtree in free agency, but they added former Ravens wideout Torrey Smith, giving Kaepernick a legitimate deep threat for the first time. Smith will be paired with Anquan Boldin, one of the NFL’s most physical receivers. The 49ers need former Pro Bowl tight end Vernon Davis to rebound after catching just 26 passes for 245 yards and two touchdowns.
San Francisco’s offensive line, which had long been a team strength, needs to bounce back, too. Kaepernick was sacked 52 times last season, and the line was in disarray most of the season. Center Daniel Kilgore missed the final nine games with a broken leg. Right tackle Anthony Davis missed nines games with assorted injuries. Right guard Alex Boone reported late because of a contract dispute and never got untracked, and he’s still unhappy with his contract. After the season, the 49ers lost Pro Bowl left guard Iupati to Arizona as a free agent. Brandon Thomas, who missed his rookie season last year with an ACL injury, should get the first shot at replacing Iupati, but he’ll battle free-agent pickup Erik Pears. Left tackle Joe Staley, a four-time Pro Bowl choice, still anchors a line that needs to regain its spot among the NFL’s elite.
The hits kept on coming during the offseason for a 49ers defense that is still solid but nowhere near the force it was a few years ago. Willis, a seven-time Pro Bowl pick, retired in early March because of chronic foot injuries. Days later Chris Borland, his backup, retired because of health concerns over concussions. Then in late May, Pro Bowl defensive end Justin Smith announced he was retiring after a successful 14-year career. Defensive end Ray McDonald was released after yet another off-field incident. The 49ers also lost two of their top three cornerbacks — Chris Culliver and Perrish Cox — to free agency. The 49ers used a first-round draft pick on Oregon defensive end Arik Armstead, but he needs time to develop. Veteran defensive lineman Darnell Dockett, a free-agent pickup, is coming off a knee injury that forced him to miss the entire 2014 season. Young D-linemen Quinton Dial and Tank Carradine might have to take larger roles.
The 49ers’ biggest loss on defense could well be Fangio, who set the bar extremely high. Under Fangio, the 49ers’ ranked as high as third and never dropped below fifth in total yards allowed.
The 49ers expect to have All-Pro inside linebacker NaVorro Bowman back in the lineup after he missed the entire 2014 season while recovering from a devastating knee injury. Starting cornerback Tramaine Brock missed most of last season with a turf toe injury but is expected to regain a spot in the starting lineup and be paired with ex-Chargers cornerback Shareece Wright, a free-agent pickup. The 49ers have one of the NFL’s top safety tandems in Eric Reid and Antoine Bethea. Outside linebacker Aldon Smith, who had 19.5 sacks in 2012, should get back on track after being suspended the first nine games last season for violating the NFL’s personal conduct and substance-abuse policies.
Punter Andy Lee, a three-time Pro Bowler, was traded in early June to Cleveland for a 2016 seventh-round draft pick. This move was expected as soon as the 49ers used a fifth-round draft pick in May to select Clemson punter Bradley Pinion, who doubles as a kickoff man. That could turn out to be a key skill, considering that placekicker Phil Dawson, who is coming off of a subpar season, struggled to kick the ball deep. As a rookie last season, wide receiver Bruce Ellington handled most of the return duties. Jarryd Hayne, a rugby superstar from Australia, was signed as a free agent and could give Ellington some competition.
The 49ers won’t have to deal with as much dysfunction this year, but they lost a lot of talent, both on the field and in the coaching ranks. Baalke did little in free agency or the draft to help the 49ers’ struggling offense. The 49ers finished third in the NFC West last year, and it’s difficult to see them finishing ahead of defending division champion Seattle or Arizona, which was second. Even holding off the last-place St. Louis Rams could be a problem.