49ers in state of disarray after loss to Raiders crushes playoff hopes

OAKLAND, Calif. -- He will coach three more games for this team, but Jim Harbaugh appears to be as good as gone. In truth, he was probably finished with the

OAKLAND, Calif. -- He will coach three more games for this team, but Jim Harbaugh appears to be as good as gone. In truth, he was probably finished with the 49ers before Sunday’s stunning upset at the O.co Coliseum, where his team was outplayed in every phase of the game by a 1-11 squad coming off a 52-0 loss to another outfit with a losing record, the Rams.

Yet there was Harbaugh, with 28 seconds to play, still coaching, still grinding, dispensing instructions to the troubled Colin Kaepernick, despite the fact the Niners were trailing 24-13 and 85 yards from Oakland’s end zone. At the end of yet another tough day at the office, one that featured five sacks, two picks against just a single touchdown pass; a 54.4 rating, Kap made a decent play, finding tight end Vernon Davis for a 10-yard gain. But, and here was the story of the day -- no, the 2014 season -- the Niners had lined up in an illegal formation. Kap was sacked on the next snap, and the game, mercifully, ended.

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Also drawing to a close, in that moment:

• Any realistic chance the Niners had at a playoff berth. Their record is now 7-6. Six teams in the NFC have better records by at least two games.

• The season of even pretending that Harbaugh will be back with this team next year. Let’s reflect for a moment on how remarkable that is. Regardless of how difficult he may be to get along with, of how strained his relations may be with GM Trent Baalke and owner Jed York, Harbaugh coached this club to the last three NFC title games. He’s won 43 of his 60 games in San Francisco. His winning percentage is .713 compared to Sean Payton's .624 in New Orleans. The Saints are 5-8 this season, and coming off a putrid 41-10 loss to Carolina. But no one’s talking seriously about the possibility of Payton getting run out of town.

But Harbaugh’s freshness date has expired. Asked after the Raiders loss, the nadir of a difficult, turbulent year, if he thought Baalke and York wanted him back, he refused to answer the question directly, choosing instead to list his “priorities” -- winning games, attending to the welfare of his players, coaches and staff, “and lastly,” his “personal professional future.”

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Asked if it was up to him -- if he wanted to return -- he replied: “My priorities are winning games.” Read: No.

How did it come to this? How did he go from “WHO’S GOT IT BETTER THAN US?” to “Whose checks will I be cashing next season?”

He invested heavily in a quarterback whose stock is now tanking. The emergence of Raiders rookie quarterback Derek Carr -- and Carr’s effortless poise in the pocket -- threw into sharp contrast the struggles of Kaepernick, who in his 42nd NFL start was a hesitant, indecisive shadow of the player who took the league by storm in 2012.

Lending spice to Sunday’s Battle of the Bay was the fact that Oakland looms as a possible landing spot for Harbaugh, who was an assistant there in ’02 and ’03, and would surely relish the chance to restore the luster to this foundering franchise, while the Niners, presumably, backslide into the decade-long oblivion from which he rescued them.

One major draw: The aforementioned Carr, who performed a vivisection on the Niners, completing 22 of 28 passes for 254 yards and three touchdowns, against zero interceptions. His quarterback rating, 140.2, was 85.8 points higher than that of Kaepernick, who after taking that sack on the game’s last play was helped up by his teammates, then greeted by Carr. There was something almost surreal to this tableau: the quarterback who was throwing into the end zone in a failed attempt to win the Super Bowl two seasons ago was now being basically consoled by the quarterback of the two-win team.

They’re going in opposite directions. One play, late in the first half, best illustrated where Kap is in his stalled career. Trailing 10-7, he hit AnquanBoldin for 16 yards, then scrambled up the middle for 17, a play that came back after the 49ers were flagged for unsportsmanlike conduct. He then found Boldin at the left sideline for 20 more yards.

On the next snap, he pulled the ball down to run, angling for the left sideline. There was a first down for the taking. Instead, Kap badly overthrew Davis, who wasn’t open to begin with. Here was his conundrum in a nutshell: defensive coordinators have largely figured him out. By “spying” and otherwise containing him, they’ve forced him to try to beat them with his arm, from the pocket. He seems to want to become that player -- as evidenced by that misbegotten throw to Davis -- but it’s not going well. He locks onto receivers, he doesn’t get far into his progression, he hasn’t been accurate. He is at once exceptionally mobile and the most-sacked quarterback in the league (43). Interpretation: he’s confused. He’s lost his mojo. And, when it suits him, his voice.

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Overheard in the press box Sunday: banter concerning the “over-under” on the word count from Kap’s postgame press conference, and whether it would exceed his churlish frosting (87 words in response to 32 questions) of the Niners beat writers four days earlier.

Following the loss that essentially extinguished their playoff hopes, Kaepernick indulged in a veritable filibuster, for him, enunciating 133 words -- on just 16 questions -- a much higher WPQ (words per query) than Wednesday's exercise in misanthropy.

One of those question asked him to explain his apparent stiff-arming of a photographer as the Niners headed into the tunnel at halftime.  “If I put something real close to your face, you’re going to try move out of the way, too,” he said.

Regardless of whether the contact was justified, the point is that Kaepernick no longer gets the benefit of the doubt. Yes, he’s done a remarkable job building his brand as a smoldering, soft-spoken rebel. But that appeal doesn’t work as well when you can’t complete more than 55.2 percent of your passes, a mark Kaepernick has failed to surpass in five of his last six games. It doesn’t work when you direct the NFL’s worst red zone offense and when you are averaging 6.1 second-half points per game -- second-worst in the league. Then people don’t think you’re a rebel. Then they arrive at different conclusions.

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Afterward, some Niners refused to rule out the possibility that their playoff hopes were still alive. Frank Gore, the team’s soulful -- and truthful -- running back, was not among them. He’s too authentic. “If we beat the Raiders, we still had hope” to eke out a wild card spot, he said. Translation: they no longer have hope. “So this is the lowest point.”

Gore is 31, three games from the end of his 10th NFL season. He sounded weary and sad, explaining that in this, the final year on his contract, “I wanted to … get a shot to be able to hold the trophy.”

There will be no Lombardi Trophy for the Niners. Not this season, not during the Harbaugh Era. The 49ers are not going to the postseason. Another way of saying it: 12 teams will have it better than them.

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