San Francisco 49ers DC Steve Wilks just didn't mesh well, which is why he had to go

Then in overtime of the Super Bowl against arguably the top quarterback in the NFL, Shanahan had to call a timeout because Wilks wanted to a run an ill-fated cover zero blitz on third-and-short.

As the first outside hire of Shanahan’s tenure with the 49ers, Wilks’ hiring at first glance seemed to be an optimistically bold decision.

After all, the 49ers ranked first in the NFL in total defense and scoring defense the season before, and they had only gotten better, adding star defensive tackle Javon Hargrave during the offseason and former No. 2 overall pick Chase Young at the Oct. 31 trade deadline.

But Wilks joined the organization with a defensive philosophy and background that differed from what San Francisco had run the previous couple of years. Wilks also didn’t bring in his own assistant coaches and he was made to work within the confines of what SF already had. 

“We committed to not only the system but the players within the system, the D-line, the linebackers,” Shanahan added. “They’d played in it for such a long time. It was my goal to not have to change all of them.”

The idea was that Wilks would pick up right where DeMeco Ryans left off before taking the Houston Texans head-coaching job, just as Ryans had picked up where Robert Saleh left off two seasons before after Saleh left to take the New York Jets head-coaching job.

And to a degree, he did. It just didn’t show when it mattered most.

San Francisco finished with the third-best run defense (89.7 yards per game) and third-best scoring defense (17.5 points per game) during the regular season. But after reaching the postseason, the 49ers allowed 149.3 yards per game and 25.6 points per game while playing from behind against both the Green Bay Packers and Detroit Lions.

Wilks is no question a good defensive coordinator, he’s just not the right coordinator for Shanahan’s system. His disastrous play-calling in the fourth quarter and overtime of the Super Bowl all but solidified that he just didn’t mesh well with Shanahan’s vision for how he wants the 49ers to play.

From the tone of his remarks on Wednesday, it seems like Shanahan plans to promote Wilks’ successor from within. Some names to keep an eye on include defensive passing game specialist Nick Sorensen, defensive line coach Kris Kocurek, linebackers coach Johnny Holland and defensive backs coach Daniel Bullocks.