AP

Not long ago, the interest of Kyle Shanahan in the head-coaching job in San Francisco was lukewarm at best. It has heated up considerably this week.

Shanahan’s spike in interest in the job resulted from the lack of interest that multiple others had, either in coaching the team or in taking the G.M. job.

It began with Chiefs director of player personnel Chris Ballard. Regarded as the team’s first, second, and third choice for the job, Ballard wasn’t interested. He asked the team to deny the request for permission to interview him for the job, apparently in order to avoid the impression that he generally isn’t interested in an opportunity for advancement.

Next came Patriots director of player personnel Nick Caserio, who didn’t want the job, either. Other candidates for the G.M. job either declined an invitation to interview or withdrew after interviewing.

The decision of Ballard and Caserio to pass on the job apparently contributed to the shift in agenda from hiring a G.M. first to hiring a coach and G.M. who will work together well. As potential members of a tag team began to bow out (starting most prominently with Patriots offensive coordinator Josh McDaniels), that plan changed as well. When Seahawks offensive line coach Tom Cable withdrew, it left Shanahan as the only candidate.

Shanahan will benefit from that situation, significantly. He’s expected to be the highest-paid first time head coach in league history, and he’s expected to have final say over the roster and the draft. Next, he’ll be directly involved in the General Manager, which makes Shanahan the clear-cut captain of the S.S. 49er.

So how did it get to this point? Despite the widespread popular belief that the 49ers are currently the most dysfunctional team in football, the thinking in league circles is that, with some tweaks, the G.M. and coaching jobs could be desirable. The impediment to attracting their preferred candidates isn’t owner Jed York; apparently, it’s Chief Strategy Officer and EVP of Football Operations Paraag Marathe.

Marathe is, as a practical matter, the Russ Brandon of the 49ers. The only difference is that the 49ers make no secret of Marathe’s influence over the football operations.

From his online bio: “On the team side, Marathe reports directly to 49ers CEO Jed York and has a significant role in major strategic decisions for the club as Chief Strategy Officer. He also continues in his long-respected role as the team’s chief contract negotiator and salary cap architect, while overseeing the team’s football analytics department.”

Put simply, Marathe has influence, along with the ear of ownership. He’s been there for 16 years, and he has transcended the bubble of accountability in which coaches and General Managers reside. And that’s precisely the kind of dynamic coaches and General Managers try to avoid.

Shanahan is embracing it because, as his final package will demonstrate, he leveraged the team’s desperation to his full advantage. Moving forward, however, it’s an elephant in the room that may be serving as an oversized anchor.