Harbaugh faces the first real controversy of his coaching career.
Let's begin with this, because it's important I put it out there for the record: I love everything about Colin Kaepernick as a player and a person.
I love his composure, his maturity, his poise, and obviously, his skill set. It's no secret that he can do things on a football field that Alex Smith and most any other NFL starter could only dream of doing.
The young fella has all the physical attributes of a young Randall Cunningham, but unlike poor Randall (my all-time favorite player, I should point out) Kaepernick isn't an egomaniac or a space cadet and he's far more coachable.
Really, I'm not sure what was more impressive, Kaepernick's 50-yard scamper down the right sideline to atone for his wayward pitch to Ted Ginn and set up the go-ahead field goal, or the way Kaepernick took full responsibility for the loss after the game, showing the kind of accountability and leadership that is a must-have from a starting quarterback.
Another thing I noticed, that may or not be significant: When Jim Harbaugh did his pregame ritual of slapping his starting QB's shoulder pads repeatedly, Kaepernick never broke eye contact with him. He wanted to show he was confident and ready for this moment, even though the evidence at hand showed that he wasn't.
Truth be told, this story really isn't even about Kaepernick, and it's certainly not a hit job on him. He's actually an innocent bystander in all this, a victim of circumstance.
To put it another way, he's collateral damage in the battle of his coach's ego vs. common sense.
What Harbaugh is doing by pledging to stick with Kaepernick as the starting quarterback of the 49ers is a disservice to the rest of the team, to his coaching staff, the owners, and most of all, the fans. It flies directly in the face of what should be the team's primary goal in the 2012 season: To compete for a Super Bowl.
Once Peyton Manning rejected the 49ers' advances in the off-season, Harbaugh and the team's brass had one simple decision to make: Stick with Alex Smith, the guy who led them to a 13-3 record and an NFC Championship Game berth the previous season or jettison Smith, bring in a veteran backup (such as Josh Johnson) and go with Kaepernick, the prized second-round pick and unquestioned franchise quarterback of the future.
By deciding to stick with Kaepernick instead of a healthy Smith down the stretch run, Harbaugh is telling the world he wants to have his cake and eat it too. He's allowing his ego to run rampant, and he's placing it above winning.
Harbaugh won't ever admit it, but he clearly cherishes his reputation as a "quarterback whisperer."
Sure, everyone knows that he discovered and developed Andrew Luck, the best quarterback prospect to hit the NFL since Peyton Manning, but the better Harbaugh story comes from way back in 2002, back when he was working for the Oakland Raiders as an assistant coach in 2002 and was assigned the task of evaluating draft prospects.
Harbaugh gave a second-round grade to Tony Romo, then an unknown from Eastern Illinois, and a sixth-round grade to David Carr, who would go on to be drafted first overall by then-expansion Houston Texans and have a extraordinarily terrible career.
You can choose to believe that Harbaugh doesn't care about the accolades, that there's no extra personal satisfaction he'd derive from proving to everyone that the guy he picked No. 36 overall in the 2011 draft—really the first big decision of his head-coaching career—is better than the one Carolina picked first overall, better than the one Tennessee picked eighth, better than the one Jacksonville picked 10th, etc.
I think that's naive. There's nobody more competitive than Harbaugh, and proving that he saw something in Kaepernick that 31 other GM's didn't is all a part of his competitive drive. It's not something he can just turn and off. Harbaugh competes when he engages in terse back-and-forths with the media. He never stops competing.
I have no doubt whatsoever that Kaepernick will eventually turn into a star quarterback, particularly if he's fortunate enough to have Harbaugh coaching him for the majority of his career.
However, for all his wondrous talent, for all his maturity and work ethic and diligence, the kid just isn't ready to lead the team to a Super Bowl run. It's no knock on him at all. It's just reality.
What Kaepernick needs is time. He needs reps, both mental and physical. He needs to experience ups and downs and to learn from his mistakes. Experience is truly the best teacher, more so than any coach can be.
Kaepernick's veteran teammates don't have time, though. They have a month, four games, and then the do-or-die playoffs.
Randy Moss didn't sign up for this, his last chance at a ring, to shepherd a kid through games. Justin Smith, 33, who's given his all for the franchise, surely didn't sign up for this. You have to wonder how veteran leaders like Frank Gore, Joe Staley, Jonathan Goodwin and Donte Whitner feel about it in private moments.
Gore's situation in particular is worrisome. He's 29, a graybeard in running-back years, and he's being worn down to a nub before our eyes. Ever since Kaepernick took over the starting job, Gore's playing time spiked sharply upward, with the coaching staff reluctant to pair an inexperienced quarterback with the shaky blitz-diagnosing skills of Kendall Hunter.
Hunter was lost for the season last week, anyway, which just caused the coaches to lean on Gore even more against the Rams, with a season-high 23 carries for a hard-earned 58 yards. Gore's left arm was hanging limply at his side by the end, but he checked back into the game because of course he did.
Harbaugh needs to decide here and now what his and the team's priorities are. If developing Kaepernick for the future is truly the most important goal above all others, then he might as well take the same road with all the other youngsters and play A.J. Jenkins and LaMichael James, who've spent all season picking splinters off their rumps.
Heck, while you're at it, start Ricky Jean Francois over Isaac Sopoaga at nose tackle and give rookie safety Trenton Robinson some snaps over Whitner.
If the goal is to make a run at a Lombardi Trophy though, then Harbaugh needs to curb his ego, drop this ridiculous Tom Brady fantasy with Kaepernick and go back to the quarterback who gives him the best chance to win here and now: Alex Smith.
It's become fashionable to rip Smith for all that he can't do, but ask yourself what's more likely, that Kaepernick plays as well as Brady did in New England's unbelievable 2001 season, or that Smith plays as well as Brad Johnson did for the 2002 Buccaneers or Trent Dilfer did for the 2000 Baltimore Ravens.
Those guys were veteran caretakers who were asked to manage games, make one or two big plays and basically not put their stellar defenses in bad spots. It's what Smith has done, superbly, in a year-and-a-half under Harbaugh's tutelage.
The ability to not screw things up gets taken for granted, but it sure looks glaring after games like the one this morning at St. Louis, doesn't it?
Part of the reason everyone is so high on Kaepernick is that he's coming into an ideal, almost unprecedented situation for a young quarterback. He's got a complete team around him, a terrific coaching staff, and had a season-and-a-half to watch and learn.
Smith, by comparison had none of those luxuries. Still, under Harbaugh he's completed, counting the postseason, 461-of-730 passes for 5,370 yards, with 35 touchdowns and 10 interceptions, a 95.6 passer rating and a 20-6-1 record in 27 starts.
To put that in perspective, a 95.6 rating would be fourth all-time in NFL history, just behind Steve Young and just ahead of Manning. (Joe Montana ranks 11th, at 92.3.)
Smith's winning percentage of .759 under Harbaugh would rank second all-time, behind Brady's .779.
Also, consider that the bulk of those numbers were compiled in 2011, a season where Smith was learning a new offense and didn't even have the benefit of mini-camps or a full training camp, thanks to the lockout.
His first real off-season with Harbaugh and a real understanding of the offense came prior to this season, and Smith has shown much improvement across the board.
Kaepernick got deserved plaudits for tearing up the Chicago Bears during his starting debut, but too much praise the following week for leading the offense to 17 points in a 31-21 win at New Orleans, where the terrific work of his defense largely got overshadowed.
Never mind the fact that beating the Saints this season has hardly been worthy of headlines. They've lost to Carolina, at home to Kansas City, and Robert Griffin III dropped 40 points on them in the first game of his pro career, also in New Orleans.
No matter how much we want to pretend that a dynamic quarterback is all that was needed to jump-start the offense, the reality is that the best driver in the world can't win the Indy 500 if he's got a Prius engine under the hood, and the 49ers just aren't built for eye-popping, highlight-inducing chunk plays.
They don't have a lightning-quick make-you-miss back in Gore, they don't have speed on the outside with Michael Crabtree and Mario Manningham, Moss is a hundred years old and Vernon Davis is always double-teamed.
It's a grind-it-out, take-what-the-defense gives offense, built to win ugly. The coaching staff is old school and don't believe in spreading it out and throwing 50 times a game and won't ever believe in it, regardless of who's under center. It could be Montana, Elway, Manning, whoever, it won't change as long as Harbaugh's in charge.
The offense is built for Alex Smith. Even the coaching staff is built for Alex Smith. Kaepernick is a round hole being forced into a square peg.
Harbaugh isn't seeing the forest for the trees, and it's threatening to ruin a promising season.