Why 49ers’ health is No. 1 on Kyle Shanahan’s Christmas wishlist

Despite spending all his time preparing for the Los Angeles Rams, 49ers’ head coach Kyle Shanahan has also had other things in mind, like what to ask Santa Claus for Christmas.

The chocolate-chip cookies and milk are ready under the Shanahans’ Christmas tree, but what is on the 49ers’ head coach’s wishlist this year? It’s pretty simple — the health of the 49ers’ players to be back in time for a Super Bowl run.

The stark contrast in the performance of the 49ers’ defense when they are healthy and when they are not is eye-opening. After the Saints and Falcons had success against the 49ers’ second-ranked defense, the narrative that Robert Saleh’s unit is only suffocating against weaker quarterbacks is starting to circulate.

During the first half of the season, the 49ers’ defense was allowing 11 points per game, which has been scaled back to 25.9 points per game in the second half. Arguably the best defensive line during the first half of the season, which generated pressure on 33 percent of drop-backs, is only doing that 20 percent of the time now.

A “no-fly zone” secondary was taking away the ball at a historic pace, averaging 1.4 interceptions per game during the first eight weeks, but only has one interception since.

So has the 49ers’ defense really started to slip against better competition? Nope. Absolutely not.

San Francisco’s defense is littered with first-round picks — from Nick Bosa to Arik Armstead to DeForest Buckner to Jimmie Ward, but the strength of their defense was their depth. The underlying heroes during the first half of the season were linemen Dee Ford, D.J. Jones, Ronald Blair III, Damontre Moore, Jullian Taylor, as well as corners Emmanuel Moseley and safety Tarvarius Moore.

The stars on the 49ers’ defense were able to shine, given the depth that stood behind them to keep them fresh. Let’s use pass rusher Nick Bosa as an example: from Weeks 1 - 9, Bosa averaged 38.4 snaps per game, but from Weeks 10 - 15, Bosa is playing 59.2 snaps per game.

San Francisco has their best pass rusher playing in 21 more snaps per game as of late, and that’s only tiring him out towards the ends of games. Hence in these close games, like against the Falcons, the pass-rush becomes nonexistent due to the lack of depth behind them. It’s a very similar trend for Armstead and Buckner, too, as there’s a dip in their production since the halfway mark in the season.

Continuing with that argument, I am a firm believer that the secondary and pass rush can benefit each other and hide the other group’s flaws. A strong pass rush can assist a depleted secondary, and shut-down corners can help a weaker pass rush.

The past few weeks, the 49ers have missed the likes of Dee Ford and Ronald Blair III on the defensive line, while missing Richard Sherman, K’Waun Williams and Jaquiski Tartt in the secondary. When both groups have injuries, it’s hard for one position group to hide flaws in the other.

Shanahan and Saleh can breathe a sigh of relief, cause Williams and Sherman will be playing vs. Rams on Saturday, helping a banged-up secondary that got torched by Falcons’ wideout Julio Jones last week for 134 yards.

Earlier this week, I decided to plot Football Outsiders’ DVOA per week to see if there are any obvious trends with the 49ers’ defensive performance. The graph is shown below, and the key is for the red points to remain as close to the bottom as possible, which means the 49ers’ had a productive day on defense.

DVOA takes into account the situation, strength of the opponent, and other factors that make it a more valuable metric than just raw defensive numbers.

If you look at the chart, the 49ers’ worst performances are against the Cardinals, Saints, and Falcons. I would throw out the first Cardinals’ game because it was a short week, Thursday night game in Arizona.

Against the Saints and Falcons, the 49ers missed multiple defenders at every level, and their poor performance was a direct reflection of that.

When the 49ers hosted the Packers and Seahawks and played the Ravens, their defensive performance (Weeks 10, 12, and 13) was above average and held the opposing quarterbacks to some of their worst performances of the season.

The theory that the 49ers’ defense has played poorly against better opposition just is not true. When they start to get healthy over the next few weeks, we will start to get a better sense of how dominant the 49ers’ defense can be at full strength.

Shanahan should not be worried about changing up schemes or trying anything different; he should continue to wish for the 49ers’ health to return, so they make a Super Bowl run.