The Jim Harbaugh era is no more. (USA Today Sports Images)
The Jim Harbaugh era is no more. (USATSI)

The Jim Harbaugh era in San Francisco has come to a close. According to a statement released by the team, the 49ers and Harbaugh mutually agreed to part ways at the close of an 8-8 season that saw them miss the playoffs for the first time in Harbaugh's tenure. San Francisco had previously gone at least as far as the NFC Championship Game in each of Harbaugh's three seasons.

Harbaugh leaves San Francisco with a 44-19-1 record that translates to a 0.694 winning percentage, the second-best winning percentage in the history of the franchise (excluding former interim coach Jim Tomsula, who went 1-0 filling in for the fired Mike Singletary in 2010). Harbaugh is widely expected to become the next coach of the University of Michigan. 

Rumors about Harbaugh's future with the team (or lack thereof) swirled almost from the jump this year after he was apparently nearly traded to the Cleveland Browns in the offseason. San Francisco then got off to a good start with a win over the Dallas Cowboys in Week 1 despite being without multiple starters, but the 49ers blew halftime leads in each of the next two weeks. They blew three more halftime leads for a total of five and were outscored by 81 points in the second half of games this season. They finished up the year 1-4 after coming out of the gates with a 7-4 record. Eventually, as the 49ers' season spiraled out of control, it became a foregone conclusion that Harbaugh was gone once the year was up.

While in San Francisco, Harbaugh's calling cards were the same power running offense and hard-hitting defense his teams ran at the University of San Diego and Stanford University. The 49ers finished on the top-five in defensive DVOA in all four of Harbaugh's seasons. Patrick Willis, NaVorro Bowman, Justin Smith, Aldon Smith and more formed the core of what was at times the most feared defense in the NFL.

The 49ers used a run-first offense for the majority of Harbaugh's time in San Francisco, but he also utilized a low-risk passing game to turn both Alex Smith and Colin Kaepernick into above-average quarterbacks for long stretches. Smith completed 64.2 percent of his passes for 30 touchdowns and 10 interceptions in 26 games under Harbaugh, steep rises from his 57.1 completion percentage and 51:53 touchdown to interception ratio before Harbaugh became head coach.

When Smith suffered a concussion in 2012, Harbaugh unleashed the dual threat of Kaepernick's arm and legs on the league. Harbaugh, Kaepernick and the 49ers' then-stout offensive line took the zone-read to new heights in a first-round matchup with the Green Bay Packers, where Kaepernick ran for 181 yards and two touchdowns, in addition to his 263 yards and two touchdowns through the air. The image of Clay Matthews spinning in his cleats as Kaepernick took off down the field time and again will never be forgotten.

Kaepernick's progression stalled over the ensuing two years, though, particularly in 2014 as the offensive line began to deteriorate under the weight of injuries, holdouts and poor play. Right guard Alex Boone held out for a new contract in training camp and never reached previous heights. Right tackle Anthony Davis missed multiple games with injury and played poorly when he was on the field; backup Jonathan Martin was arguably worse. Center Daniel Kilgore got hurt and his replacement Marcus Martin did not fare well at all. Left guard Mike Iupati was merely good, as opposed to an All-Pro level talent.

Kaepernick was prone to holding the ball for too long while waiting for receivers to get open. Those receivers -- Anquan Boldin excepted -- rarely got open themselves. Vernon Davis became little more than an afterthought. The running game, led by Frank Gore and supplemented by rookie Carlos Hyde, was worse than it had been at any time in the Harbaugh era.

Harbaugh's team also had numerous run-ins with the law, notably defensive end Ray McDonald's domestic violence case that garnered a lot of media attention throughout this season, as well as Aldon Smith's high-profile issues with both substance abuse and personal conduct. According to Bleacher Report's Mike Freeman, Harbaugh came to believe that the behavior problem in the NFL is "almost impossible to fix" and there was a divide between Harbaugh and the front office on how to handle players with disciplinary issues. 

That theme of Harbaugh butting heads with the front office is one that came up numerous times while he was in San Francisco, with various reports stating at different times this season that there was friction in the relationship between Harbaugh and general manager Trent Baalke. In the end, the relatonship was no longer workable for any of the parties involved, and they agreed to go their separate ways.

How do 49ers players and personnel feel about Harbaugh's departure?

As we detailed this week, Frank Gore is none too happy about it. He feels Harbaugh is the best coach he's ever had.

Gore's sons didn't want to see Harbaugh go, either:

Jim Harbaugh says goodbye to Frank Gore in 49ers locker room.

A photo posted by Matt Maiocco (@maioccocsn) onDec 12, 2014 at 5:17pm PST

Meanwhile, Anthony Davis was all for Harbaugh's ouster, and apparently isn't too fond of offensive coordinator Greg Roman, either.

Running back Alfonso Smith chimed in:

Tackle Jonathan Martin:

Linebacker Dan Skuta:

Receiver Anquan Boldin:

Quarterback Colin Kaepernick:

Minority owner Gideon Yu:

What does this mean for the Raiders?

Oakland was expected to chase Harbaugh if he became available, but with the Michigan move reportedly all but announced, the Raiders will have to regroup. They reportedly intend to interview Arizona defensive coordinator Todd Bowles and have interest in Stanford head coach David Shaw, though more names will presumably be floated in the event they decide to part with interim head coach Tony Sparano.

One factor will likely be the future of general manager Reggie McKenzie, whom Davis likes and, according to CBS Sports NFL Insider Jason La Canfora, continues to support, but who has been largely ineffective in his role.

Was there another Alex Rodriguez sighting at Harbaugh's last game?

You bet.

Where will San Francisco turn next?

According to our La Canfora, the 49ers have a whole lot of names in mind for their next head coach. In-house candidates include defensive coordinator Vic Fangio and defensive line coach Jim Tomsula. According to La Canfora's report, Tomsula is "viewed internally as a very viable candidate to replace Harbaugh."

If the 49ers look outside the organization, Patriots offensive coordinator Josh McDaniels and Broncos offensive coordinator Adam Gase are expected to be candidates, as the Niners reportedly like the idea of hiring a bright, young offensive mind.

UCLA's Jim Mora, who has a relationship with 49ers acting owner Jed York, is also in the mix. Mora is 28-11 in three seasons at UCLA and was previously the head coach of both the Atlanta Falcons and Seattle Seahawks, where he compiled a 31-33 record.

Whoever takes over for Harbaugh will need to revamp an offensive line that absolutely fell apart this season, and also rebuild Kaepernick's confidence. A probable shift to Carlos Hyde as the lead back is in order, and Kaepernick needs weapons on the perimeter beyond Boldin because the guys on hand this season just didn't cut it.

San Francisco's defense has a lot of talent at linebacker in Willis, Bowman and rookie sensation Chris Borland, but Justin Smith is considering retirement and the secondary needs tending. It'll be some work to get San Francisco's roster back up to snuff in the NFC West.