THERE THEY sat on the suite level of CenturyLink Field, a row of 49ers employees wearing suits and sour expressions. Below them, a marauding Seahawks defense was putting the finishing touches on Seattle's fifth win over San Francisco in their last six meetings, in the process eliminating the visitors from playoff contention. None of the suits seemed quite so miserable as general manager Trent Baalke, who'd spent the second half startling those seated near him, slamming his palm on the table in response to particularly cruel reversals of fortune.

The coup de grace came with 2:32 left in the game: Trailing 17--7, San Francisco gave up the ball on downs. To Baalke's left, team president Paraag Marathe stood wordlessly, gathered his possessions and strode to the elevator. Moments later, Baalke lowered his head into his folded arms, a portrait in dejection. Which, upon further review, didn't make complete sense.

His team had lost, but Baalke had won. The GM has emerged triumphant in a power struggle with coach Jim Harbaugh, who despite guiding the 49ers to the last three NFC title games is on his way out. A Super Bowl run likely would have defanged Baalke and kept the coach in place for at least the fifth season of his five-year contract. But it's been obvious since Thanksgiving that this deeply dysfunctional club would be a long shot to eke out even a wild-card berth. That evening marked the 49ers' first loss to the Seahawks this season, those defeats bookending a head-scratching 24--13 loss to the 1--11 Raiders. So dispiriting did CEO Jed York find that beatdown—a 19--3 no-show that ended with Niners nemesis Richard Sherman devouring a postgame drumstick at midfield of Levi's Stadium—that he apologized to fans via Twitter, throwing his coach under the bus and leaving little doubt that Harbaugh would be gone after this season.

How did things get to this point? It was only four months ago, at training camp, that York was downplaying differences between the dueling alphas, Harbaugh and Baalke. "They might have a little different philosophy on how to get there," he told SPORTS ILLUSTRATED, "but they're on the same page. And the five percent they're not, it's healthy. They should be arguing and battling it out." Those battles, predominantly over how to populate the 53-man roster, were all but assured upon Harbaugh's arrival. He replaced Mike Singletary, who after being hired by York in 2008 was granted final roster approval—despite Singletary's lack of head coaching experience. That experiment, it's believed in the 49ers' halls, was a grievous mistake. Upon luring Harbaugh away from Stanford in '11, Baalke and York offered him a five-year, $25 million deal—but they did not offer him control of the roster. Heated arguments ensued. The club preferred to keep them from the public view, though Harbaugh didn't always cooperate. He was not above the occasional attempt to influence a contract negotiation through the media, such as the presser last year where he declared, in reference to a certain player, "Pay the man!"

"I don't think there are many better [GM-coach] combinations than Jim and Trent," York insisted in August. "They realize it might not be perfect, but they really respect each other and they do like working together."

If that was ever true, it stopped being so early this season. The Niners lost two of their first three games, then barely stole a win over the Eagles despite Philly's failing to score an offensive TD. ESPN's Trent Dilfer and the NFL Network's Deion Sanders reported that Harbaugh was losing the locker room—accounts hotly disputed by many of the players in question. Asked last week if Harbaugh still had the room, guard Mike Iupati replied with mild exasperation, "Yes, he still has the room. He never didn't have the room."

Of course there are disgruntled 49ers. But many others echoed their loyalty, including beleaguered quarterback Colin Kaepernick, who admitted after Sunday's loss that Harbaugh's imminent departure is "not something I can fully wrap my mind around."

Harbaugh, who at 50 is among the NFL's younger head men, would be the hottest item in the coaching market this off-season—that is, if the 49ers don't trade him, as they tried to do with the Browns 10 months ago. (Harbaugh can't be traded anywhere without his green light.) "Wherever Jim goes, he'll have control of the 53," says a source close to the Harbaugh family. "And he'll do what Pete Carroll did with the Seahawks: He'll hire a GM under him. I think Jim wants that kind of setup, and he's not gonna get it [in San Francisco]."

The world will be Harbaugh's oyster. Or, more accurately, his olive. As the players on his next team will soon discover, a dearth of anything—sacks, TDs, receptions for an underutilized receiver—will prompt a retelling of the Parable of the Olive Jar: You open up a new jar of olives, turn it upside-down, but no olives come out, they're packed so darn tight. But pluck one out, and next thing you know, they're flying out. Harbaugh will praise his next squad as "mighty men," imploring them to move on from victories with "humble hearts." Like every coach, his store of anecdotes and sayings is finite. Over the course of several seasons, his act may grow thin.

One theory has it that the coach is a turnaround specialist whose freshness date expires after a few seasons. In 2007, he took over a laughingstock Stanford program coming off a 1--11 campaign. Four seasons later the 12--1, Andrew Luck--led Cardinal steamrolled Virginia Tech in the Orange Bowl. But by then, Harbaugh's intensity and lack of politesse had some people inside the program hoping he'd win enough games to get another job.

"I wasn't one of those people," says former Stanford athletic director Bob Bowlsby, who hired Harbaugh and worked hard—but ultimately failed—to retain him. Harbaugh was not ... low maintenance. To galvanize the squad, to create a dynamic of "us versus them," Bowlsby recalls, Harbaugh would not hesitate to pit the team against "the opponent, or the conference, or the athletic director." That said, he concludes, Harbaugh's reign "was a great four years. There's a lot of magic in his method."

He very well may recover it, but there's no denying that Harbaugh lost a little magic in 2014. He's a superb motivator with a sharp offensive mind. He surrounds himself with quality assistants, for the most part, and stays out of their way. But one of his strongest suits, his reputation as a nurturer and developer of QBs, has taken a hit as Kaepernick, his handpicked signal-caller, struggled through a season of regression.

The postmodern, biceps-kissing, dual-threat QB-of-the-future who shredded and bewildered teams in 2012 and parts of '13, who has four playoff wins and came within one completion of winning a Super Bowl, has been solved by opposing defensive coordinators. They spy him and otherwise contain him. They force him to beat them with his arm, a feat he's found increasingly difficult this season. He ranks outside the top 20 in completion percentage, first-down percentage and passer rating.

Quarterbacks achieve greatness by mastering a number of traits to consistently perform at a high level, says Greg Cosell, a senior producer and analyst at NFL Films who has broken down video of every 49ers game for the past four years. "And one of the least important of those traits is the ability to run around."

Cosell describes Kaepernick, 27, as a "predetermined" passer who doesn't get far into his progression. He's quick to pull the ball down and run. He's at once exceptionally mobile and the most-sacked (49) QB in the league, a testament to his confusion. Kaepernick, Cosell concludes, "is not advanced at all in the nuances of playing NFL quarterback."

As one NFL quarterbacks coach puts it, every young passer comes into the league with a unique set of weapons; he can get by with those tools for a year or two, but eventually defenses adjust—and then it's up to the QB to do the same. Tim Tebow couldn't do it. The days of reckoning for EJ Manuel and Geno Smith are fast approaching. While Kaepernick hasn't entered that endgame, he needs to keep evolving, to get a firmer grasp on how his play design interacts with the coverage he reads. "He's not very good at that," says Cosell. Several times per game Kaepernick will flee the pocket the moment he reaches the top of his drop-back—the opposite of how pocket passing is supposed to work.

Kaepernick's accuracy is also inconsistent, usually a by-product of inconsistent mechanics. While he can be a highly effective runner, he's stiff and straight-legged when he leaves the pocket, with little wiggle or change of direction. Surprisingly, for a quarterback who moves so much, he doesn't throw well on the move.

The 49ers' next coach will probably want to bring in his own quarterback, if not to supplant Kaepernick, to at least compete with him. The team has some flexibility here. While the contract Kap signed in June made for splashy headlines ("as much as $126 million over seven years"), it's actually a team-friendly, pay-as-you-go arrangement allowing the Niners to cut him whenever they wish. That day isn't coming up anytime soon. Kaepernick may not be as bad as he's often looked this season—there's no doubt that number 7's job has been made much harder by a leaky, banged-up, underperforming line that struggled to sustain a running game.

For a half or so on Sunday, the 49ers' backfield was not in chaos. Kaepernick, Frank Gore and Carlos Hyde combined for 104 first-half rushing yards and engineered an 11-play, 85-yard TD drive that put the visitors up 7--3 at halftime. It was the best Kaepernick had looked in a month.

But the wheels soon came off. Gore left in the second quarter with a concussion; Hyde sprained his left knee. With Kaepernick handing off to fullback Bruce Miller and third-string running back Alfonso Smith, they crossed Seattle's 45-yard line just once in the second half. "We don't make excuses," wideout Anquan Boldin said afterward. "Everybody that's on this team deserves to be here, and we expect guys to perform when they're in there."

One of the reasons Harbaugh will be gone after this season is that his masters believe he underachieved with the talent they'd collected for him. It's only fair, however, to point out the holes in that roster: Gore, the spiritual leader and warhorse, is old (31), but not as old as Boldin (34), the team's most productive receiver. Michael Crabtree has lacked an elite burst since tearing his right Achilles in May 2013. The Niners need a speed receiver to take the top off defenses. Tight end Vernon Davis, the guy whose job that used to be, has spent large chunks of this season in the Witness Protection Program. And it doesn't help that the club's front office whiffed in the '12 draft. Only one player from that class is still with the team.

Contrast those graying 49ers to this core group of Seattle's finest: Quarterback Russell Wilson; defensive backs Richard Sherman, Kam Chancellor and Earl Thomas; and linebacker Bobby Wagner are all 26 or younger. The Seahawks aren't just good. They're going to be good for a long time.

Who knows about the Niners? "I'm not sure what the problems are over there," said Pete Carroll, the Seahawks' coach, an hour after the game. "All I know is that someone's going to get a really good coach."


PHOTOPhotograph by John Biever For Sports IllustratedNINERS, EIGHTY-SIXED Harbaugh and his QB enjoyed a fast start—21 wins in their first 28 games—but it now feels as if they were built for short-term rather than prolonged success. PHOTOJEFF CHIU/APKAP CRUNCHED Baalke and Harbaugh (left) once coexisted peacefully, but now their relationship appears as adversarial as the Seahawks-Niners rivalry, which on Sunday saw Kaepernick sacked six times. PHOTOJOHN W. MCDONOUGH/SPORTS ILLUSTRATED[See caption above]