Bad news, 49ers fans. Getting rid of general manager Trent Baalke and coach Chip Kelly wasn't enough to solve your team's problems. The 49ers now suffer from two lingering conditions: Post-Chip Kelly Disorder (PCKD) and Baalke Deficiency Syndrome (BDS).
PCKD is caused by the peculiar, long-term effects of Kelly's system on players, particularly younger players. Not only do Kelly's teams run schemes that are unlike any other in the NFL, but they also train differently, practice differently and are taught differently in team meetings.
Kelly's young offensive players often lack basic understanding of standard NFL tactics and techniques, the kind that are taught in conjunction with huddling, traditional play-calling, operating a conventional offense and so forth. Even veterans backslide a little bit. Eagles receivers Nelson Agholor and Jordan Matthews struggled with the basic mechanics of route-running and pass-catching this season, their development stunted by Kelly's scheme and training style. The 49ers have a bunch of young linemen who may be in the same boat.
Kelly's defenses, meanwhile, end up both shell-shocked from being on the field for about two hours every Sunday and hampered by a full year of uptempo practice methods that are tailored almost exclusively to the needs of his offense.
The good news is that Kelly had only one year to cause damage in San Francisco, unlike the three growth-inhibiting years he spent in Philadelphia. The bad news is that the 49ers' PCKD is compounded with a chronic case of BDS.
As you might guess, Baalke Deficiency Syndrome is caused by years of Baalke's boldly counterintuitive drafting, mixed with the kind of blatant boardroom skulduggery that makes a franchise unappealing to both its own veterans and available free agents. Baalke gave Kelly a roster with little that was even worth damaging.
Thanks to BDS and PCKD, the 49ers ring in 2017 with no general manager, no head coach, no coaching infrastructure worth salvaging, an enigma where their franchise quarterback should be, no wide receivers, about 40 percent of an NFL-caliber offensive line, a dusting of quality-but-demoralized (and injured, in many cases) veterans on defense and almost no blue-chip talent in the pipeline at any position that will make a difference anytime soon.
Just about every veteran building block worth mentioning—NaVorro Bowman, Joe Staley, Tramaine Brock, Vance McDonald, Ahmad Brooks, Colin Kaepernick—arrived before Baalke and Jim Harbaugh drew a line down the middle of 49ers headquarters in 2014. That means that the 49ers' best players are getting old, expensive in many cases and about to play for their fourth coach in four years.
A double whammy of PCKD and BDS cannot be cured easily.
The most tempting treatment for these conditions is to hire an Old School Football Guy, the older-school, the better. When the Eagles couldn't see eye-to-eye with Tom Coughlin, the Oxford University of old-school football guys, owner Jeffrey Lurie enacted a full-scale Andy Reid-style reboot. Ousted general manager Howie Roseman returned to undo Kelly's loopiest moves, Doug Pederson arrived as a Reid surrogate and the Eagles tried to pretend that the Kelly era never happened.
Niners owner Jed York isn't going to be able to lure Harbaugh back, even if he wants to. There are plenty of Old School Football Guys out there for York to woo, from Coughlin, Mike Shanahan and Sean Payton through next-generation options like Kyle Shanahan. But the 49ers cannot make the mistake of thinking going "old school" is an end or solution in itself.
The staunch traditionalist who mutters establish-the-run cliches and sneers at analytics, sports science and no-huddle tactics will sound pretty sexy to York when he is on the Kelly-Baalke rebound. But the 49ers won't get better just by doing the opposite of what made them bad.
The guy who hates all new ideas could also turn out to be a guy with, well, no new ideas. The jury is still out on Pederson in Philly; he restored calm, but he often approaches basic football questions—like hitting during practices or going on fourth down—as if he has never thought of them before. York cannot hire some fake Harbaugh who talks a good game, only to discover he handed his team to a scarecrow in khakis.
Owners like York get into Baalke-Kelly predicaments because they think in terms of "guys": Old School Football Guys, Wunderkind Football Genius Guys, Famous Guys. They yoke their franchises to two or three football masterminds, then watch them all pull in different directions.
The cure for PCKD and BDS is thinking in terms of structure, not saviors. The 49ers must do the boring stuff: Hire a personnel executive who is all about scouting reports and budgets, a coach who jells with the executive, coordinators whose schemes/temperaments/reputations complement the coach and so on, even if none of the individual moves appear particularly bold or brilliant.
Then they've got to do the tedious stuff, examining how to change the team.
* The 49ers must move on from Kaepernick. Yes, he has put up credible numbers in recent weeks. Yes, he still has talent to burn. And no, he's not some sociopolitical land mine that blows up locker rooms. But he'll be playing for his fourth coordinator in four years in 2017, having bounced from Greg Roman's run-heavy system to Geep Chryst's Roman-lite to Kelly's allegedly creative system (running the same five plays over and over again, but really fast) to who-knows-what. A lot of bad habits and contradictory instructions have piled up in his mind and body. The story of the next regime cannot be the story of what to do with Kaepernick, trying to rebuild Kaepernick, waiting for Kaepernick or whatever. Everyone deserves a fresh start. Especially Kaepernick.
* The 49ers must give the defensive veterans some hope. Players like Bowman remember being mentioned in the same breath as the Seattle Seahawks. This year, they looked like stumblebums thanks to Jim O'Neil's ineffective system and Kelly's no-rest-for-the-weary philosophy. The 49ers could try to bring back former defensive coordinator Vic Fangio as head coach, or interview respected coordinators like Teryl Austin or Jim Schwartz. At the very least, the defense needs reason to believe it can be great again before the veterans retire.
* The 49ers must take self-scouting seriously. Only a handful of Baalke players have proved they belong in the NFL: DeForest Buckner, Arik Armstead, Jaquiski Tartt. Are any of the young linemen (Josh Garnett, Trenton Brown, John Theus) likely to get better? What about defenders like Eli Harold and Rashard Robinson? Did Baalke hit on any pick after the second round since Harbaugh left? Post-Chip Kelly Disorder makes these players hard to evaluate, even internally. Success or failure in Kelly's hinky schemes and practice drills may not translate to a more conventional system.
These are all daunting tasks. Whether he pursues a big-name "guy" or takes a more systemic approach, York must find a new regime both willing and capable of doing lots of dirty work and making some potentially unpopular decisions (Kaepernick). York must also convince the newcomers that this won't become Jed York's Flying Circus. Clearing away both Baalke and Kelly was a wise first step on that front. Both would happily continue executing office intrigues if he succeeded in ousting the other. York must now prove he can foster professionalism, which for York mostly involves staying out of the way.
The only real cure for PCKD and BDS is time. It will take a full year to start looking like an NFL team again, then another year to get halfway decent. This mess was three years in the making and will take at least as long in the cleaning.
But the good news is that there is no more Baalke, no more Kelly, no more Baalke vs. Kelly, no more 49ers vs. themselves. The cure is no worse than the sicknesses themselves. Just don't expect to feel good right away.
Mike Tanier covers the NFL for Bleacher Report. Follow him on Twitter @MikeTanier.