The 49ers have been able to rely on their defense year in and year out because they have been such an elite unit. The Niners defense ranked no lower than 5th in yards allowed over the past 4 years. Then the 2015 offseason happened.
As Eric Mangini has stated, the Niners can't just replace Aldon Smith. The skill set and production that he had while he was on the field is something that put him in the upper echelon of pass rushers in this league. It is now the job of the coaches to find out what the team can do to try to fill in the void left by #99 and most importantly, win games.
I want to reiterate that there is still a significant amount of talent on this team and on the defensive side of the ball. NaVorro Bowman is back, Eric Reid is healthy again, Tremaine Brock (who actually has better ball skills than Chris Culliver or Perrish Cox had) is healthy again. The defensive line returns Glenn Dorsey and the underrated Ian Williams. Just via return from injury, the 49ers have 5 starters back in the lineup. There have also been the additions of Darnell Dockett, Shareece Wright, Arik Armstead and Eli Harold (who have drawn positive reviews over the first week of camp) through free agency and the draft.
This defense doesn't have to be the best unit in the world; they just have to be good enough to win games. It will be on the coaching staff to fit the scheme to address both the losses the defense has incurred and the new personnel.
As noted with the offense in Part 1, here are some things the coaching staff can do to put the defense in the best position to win games:
Substitute early and often
A huge part of why the 49ers defense couldn't stay healthy last year was the amount of snaps that the starters were having to play. It was well known that Vic Fangio didn't like to substitute much, especially on the defensive line. Justin Smith and Ray McDonald rarely, if ever, got breathers. In the end, the combination of long practices, lack of substitutions and amount of games played over the last 4 years (no team played more games than the 49ers from 2011-2013) caught up with this group.
The silver lining in all of this was the play of Aaron Lynch (6 sacks), Tank Carradine (3 sacks in 3 starts), Quinton Dial and Chris Borland. They were given a shot as a result of injuries and performed admirably in the place of their fallen teammates. They brought much needed youth and speed to the defense and helped keep the 49ers in several games when the offense was struggling. We would never have known what they could do if they were sitting on the bench.
Basic football correctly suggests that substitutions can keep players fresh and also create mismatches on the field. This is exactly why we have pass rushing specialists who come in on passing downs - much like Aldon Smith did in his rookie year and Aaron Lynch did last year. Based off of the positive reviews they are getting out of camp, I expect to see a lot of Eli Harold and Arik Armstead.
Subbing out a linebacker for a defensive back on passing downs can match speed with speed when the offense goes with multiple wide receivers, instead of asking a linebacker to cover a receiver. It felt like too often, our linebackers were asked to do more than they should have because their names were Patrick Willis and NaVorro Bowman, and because they were the best linebacker tandem in the league. It's not an accident that Willis wore down; the coaches will need to adjust the scheme by using substitutions to make sure this doesn't happen with Bowman, or the rest of the defense. Depth is one of the strengths of the team this year and I hope they utilize it.
Bend but don't break: More zone coverage
To me, the biggest reason the 49ers should use zone coverage is to prevent the big play. Look, the Niners aren't going to win many games that turn into track meets. It's too much to ask of the offense to come back and answer a 60 yard touchdown from the opposing quarterback with one of their own on a regular basis. The defense will need to keep the score low to keep the offense within striking distance.
Playing zone also means that the defense will be able to double certain receivers to take them away, as opposed to blitzing all the time, which will take some help away from coverage and leave corners 1-on-1 on the outside. The opposing quarterback will need to find another option once his number 1 read is taken away, which gives time for the pass rush to get there. This does put extra pressure on the defensive linemen to get to the quarterback because they have little to no help, but hopefully the additional time taken for the quarterback to read the defense before throwing will help.
The idea is to make the opposing offense play in a 10 yard box. By only giving the opposition the choice of trying to complete shorter passes, the defense will force them to make more plays to get into scoring range. Shorter passes are usually thrown where there is more traffic, which means more opportunities to take the ball away. While this does mean that the 49ers possessions will be limited, it also means that the opposing offense's possessions will be limited as well. Ultimately what it means is that less points will be scored and the game will remain close for longer, giving the Niners a better chance at earning a victory.
Blitz smart
Just because the 49ers lost their number one pass rusher doesn't mean that Eric Mangini all of a sudden has to get blitz-happy. While offensive tackle Joe Staley did say that the defense is blitzing far more than in past years, I believe the purpose of that is to get the offense ready for what they might see this season.
We all know that sending extra pressure takes men away from coverage and opens up the big play opportunity for the offense. It can leave Wright and Brock by themselves on the outside and that's bad news when you're playing the likes of Aaron Rodgers and Ben Roethlisberger, who are not fazed by extra pressure because they know exactly where to go with the ball.
On the flip side, there will be several games where the 49ers play quarterbacks who are either inexperienced (Johnny Manziel), or not very mobile in the pocket (Joe Flacco, Carson Palmer, Jay Cutler, Matt Ryan). Sending the extra pressure can fluster a young quarterback and make even the savviest of veterans get rid of the ball before they want to. This translates into opportunities to create turnovers and can end drives quicker without letting the opposition string together a bunch of plays.
Blitzing is effective in certain situations but not needed in others. For example, if the opponent has the ball on their own 12 yard line and it's 3rd and 12, there's no need to blitz because they're more likely to play it safe so close to their own end zone and throw an underneath pass or run the ball. However, if the Niners are showing that they are continually getting to the quarterback by blitzing, I would hope that they don't deviate from that plan. Another benefit is that it forces the offense to bring in extra protection, which can take receivers out of their patterns to come in and block, leaving less targets for the quarterback to throw to.
The defense has been the strongest unit on the team for the better part of a decade. This year, with all of the roster turnover and without Aldon Smith, the defense needs more help than ever from the coaching staff and from the offense scoring points. It's worth noting that everything I've listed above was done to some extent by Vic Fangio, who I am a huge fan of. He was able to implement his scheme because of the players that he had. This current bunch would be best suited to use some of what worked from the past and combine that with a strategy that keeps the defense healthy to give them the best chances of coming out on top when the clock hits :00.