It wasn't supposed to be this way.
Coming off of three straight NFC Championship games, the window to win a Super Bowl still looked to be wide open. After all, on paper the offense looked as dangerous as any year since Jerry Rice wore red and gold, and this was the season the unit was supposed to carry an undermanned defense.
No one could have foreseen it all falling apart the way it has, and the aftermath of a possibly distracted coach and an underachieving quarterback have left us asking questions.
What am I supposed to think about Jim Harbaugh?
His record speaks for itself doesn't it? He took a franchise that was floundering in obscurity and has gone 43-16-1 to date, as well as a Super Bowl appearance and the aforementioned three NFC Championship games.
But ask yourself, has Harbaugh done a good job this season?
The 49ers are 7-5 and lucky to be that. Out of those seven wins, only two of them have been by more than a touchdown. They seem to play to the level of their competition most weeks, and have been embarrassed on more than one occasion against top tier teams (i.e. the Denver Broncos and Seattle Seahawks).
The offense is an utter disaster and even though you could rightfully blame offensive coordinator Greg Roman for that, this is Harbaugh's team. He's the one who has assembled the offensive staff and had final say on the play calls.
And don't fool yourself, this offense has been atrocious.
The 49ers have 22 offensive touchdowns this season. The only teams that have less are the Minnesota Vikings, Jacksonville Jaguars, New York Jets, and Oakland Raiders.
Those teams have a combined 10 wins.
Once a run first team, the 49ers seem to have an identity crisis from series to series, and that inconsistency is part of the reason their two lead runners (Frank Gore and Carlos Hyde) are each averaging under 4.0 yards a carry.
It's hard to believe that Harbaugh has forgotten how to coach, but you have to wonder if his contract and the issues he reportedly has with the front office have bled into his work.
It looks like anything short of a Super Bowl (which is laughable at this point) will result in him leaving San Francisco.
Would a new contract get him back on track? Maybe. But that appears to be a long shot right now.
Just remember, as disappointing as this year feels at 7-5, San Francisco only had two winning seasons in the 12 years before Harbaugh got there.
If the fences can be mended, it would benefit all parties to do so. But the offense would still have to be addressed. Would Harbaugh part ways with Roman?
The last four games will tell a lot about where this team is mentally, and if the Harbaugh situation is getting into the minds of the players. If they continue to falter, it's safe to say the off the field issues have ruined what could have been a magical season.
Is Colin Kaepernick really the answer at quarterback?
Less than two years after being the difference maker during the team's run to the Super Bowl, Kaepernick looks lost behind center and is a major reason why the 49ers are underachieving. He's been given the keys to a Porsche, and while he doesn't wreck it, he can't seem to get it over 30 MPH either.
To be fair, has the offensive line been a shell of itself? Absolutely...and that does have to factor in. The 49ers have the second highest sack percentage in the NFL at 9.0, although that ranking shouldn't come as a surprise.
Since 2011, they have been in bottom six or worse in that department, and never finished lower than 8.6 percent. What's more surprising is how inconsistent the running game has been, which has always been a support system for Kaepernick and strength of the offensive line.
But there in lies part of the problem. The 49ers have needed Kaepernick to be the "franchise" quarterback they are paying him to be, and make the people around him better. He simply hasn't done that.
Kaepernick is freakishly athletic, and it's scary to think how good he can be if he ever put it all together.
The issue is, he's not much of a passer right now.
Kaepernick doesn't seem to see the field before or after the snap, and struggles to stay in the pocket and progress through his receivers past the first read. It's not uncommon for young quarterbacks to struggle in this department, but Kaepernick seems to be regressing in his third season.
His yards per attempt (7.3) and yards per completion (11.9) are the lowest of his career, and he's taken a league leading 38 sacks.
The funny thing about all of this is that Harbaugh and Roman turned Alex Smith's career around by playing to his strengths, yet they continue to try and make Kaepernick something he's not: a pocket passer.
It's understandable to fear injury with a player like Kaepernick, but the alternative is what you have now, which is a non-functional passing offense in an era where rules are designed to help teams pass the ball.
In the end, whoever the coach is has to make a decision on what Kaepernick is and what he (realistically) can be.
Because the day is coming where his contract will continue to escalate and the team won't be able to have the weapons they do now.
And if Kaepernick can't make do with more, can you imagine how bad he might be with less?
