49ers entering uncharted territory

The 49ers are heading into the last two weeks of the regular season in a very unfamiliar position.

SANTA CLARA, Calif. - For the first time in four years, the San Francisco 49ers are not playing meaningful games as they approach the end of the regular season.

These final two weeks for San Francisco with games against San Diego and Arizona have the feeling of purgatory, given head coach Jim Harbaugh's lame-duck status heading into the team's uncomfortable offseason that will feature a drastic organizational shift.

With Harbaugh likely gone, either via trade or firing by CEO Jed York, a multitude of questions arise going forward, including whether or not the team's next coach can hold the championship window open after Harbaugh was so successful at constructing the window in the first place.

"It's not something I can fully wrap my mind around why that would be the situation," quarterback Colin Kaepernick said Sunday. "(Harbaugh) has my full support not matter if he is here of somewhere else. I hope he is back here I think he is a great coach."

Kaepernick's support of Harbaugh has been staunch in recent weeks in response to all the chatter surrounding his future with the team. After all, it was Harbaugh who went to Kaepernick and help design an offense catered to his athleticism. Kaepernick as an unknown weapon in an unknown offense helped the 49ers reach - and nearly win - the Super Bowl in 2012.

[Related: Harbaugh: Gore “feeling good” after concussion]

But veering away from that offense this season might have been Harbaugh's undoing in Santa Clara. After San Francisco inked Kaepernick to a lucrative - albeit year-to-year - new contract extension that could pay him upwards of $115 million if all the stipulations are fully realized, Harbaugh and his offensive staff went into the year wanting to put more on Kaepernick's shoulders.

In doing so, Kaepernick's faults as a pocket passer were put on display and he became susceptible to pressure, getting sacked an NFL-high 49 times through 15 weeks, unable to shake his habits of trying to make plays with his legs which put him on the fast track to stardom in his first season as starter.

Couple that behind an offensive line that struggled mightily with cohesion for the first time in front of Kaepernick, and San Francisco's offense was unable to evolve into the more diverse crew that Harbaugh and coordinator Greg Roman thought would help beat the Seattle Seahawks.

Add a pinch of struggling (Vernon Davis) and injured tight ends (Vance McDonald, Derek Carrier, and Garrett Celek) to the mixture, and the tight-end centric scheme was hindered in a significant way.

With 29 starts to work with, opposing teams were at an advantage as well, coming into 2014 with knowledge of Kaepernick's tendencies, including a better understanding of his early reads on passing plays. Perhaps no team knew those tendencies better than Seattle, who drove the fork in San Francisco's playoff hopes last week.

In their two matchups with their rivals, the 49ers managed as many points (10) as sacks allowed, with their record falling to 7-7. The last three weeks have also featured Harbaugh's first three-game losing streak since becoming an NFL head coach.

So where do the 49ers go from here with two games remaining in Harbaugh's uncomfortable situation?

"Well, we have a lot to play for," Harbaugh said. "We’re going to play these next two games like our lives depend on it. So, yeah playing for a winning season, playing for each other, playing for the team, playing for the honor of the game."

The Chargers (8-6) come to Levi's Stadium Saturday a game out of the playoff hunt after losing last week at home to the Denver Broncos 22-10.

"(We) play for one another. Play for a winning record," veteran safety Antoine Bethea said. "To go into the offseason on a high note. We still do have something to play for. Play for your pride."

Next story:

49ers add linebacker Bishop

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