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How the San Francisco 49ers Became the NFL's Team to Beat in 2013

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 How the San Francisco 49ers Became the NFL's Team to Beat in 2013
Kyle Terada-USA TODAY Sports
49ers GM Trent Baalke assembled one of the NFL's best teams from the ground up.

Coming off back-to-back division crowns, two conference title games and one Super Bowl berth, the San Francisco 49ers are one of the NFL’s scariest teams heading into the 2013 season.

In two years under head coach Jim Harbaugh, the 49ers have achieved one of the greatest turnarounds in recent memory, ranking No. 11 in points for and No. 2 in points against in consecutive seasons from 2011-2012.

This has equated to a 24-7-1 regular-season record for the former play-caller from Stanford and final pupil of Bill Walsh. It is hardly a coincidence that since Harbaugh’s induction, the 49ers have been winning nearly 80 percent of their games, per Pro Football Reference.

The franchise has hardly made a single questionable decision during his tenure.

Now, while the head coach is at the forefront of this resurgence, he is more like the final component. A lot contributed to the Niners' recent rise to prominence. A team this dominant does not get that way overnight, or in a shortened league year for that matter.

This ballclub is scary because it is the total package. They flaunt a stacked roster, an innovative coaching staff, a brilliant front office, a young supportive owner and a promising young talent behind center.

This is the story of how the 2013 San Francisco 49ers came to be. 

 

The Down Years from 2005-2010 

Greg Trott/Getty Images
Trent Dilfer (left) and Mike Nolan (right) on game day in 2007.

1. Coaching and Logistics

Out of 32 ballclubs in 2004, the 2-14 Niners were the bottom-ranked unit in team efficiency, per Aaron Schatz of Pro Football Outsiders. In what had unmistakably been the weakest division in pro football, San Fran was proclaimed the worst of the bunch. 

That's a tough pill to swallow. 

In a rebuilding year in 2005, the organization hired Mike Nolan, who was fresh off a three-year stint as defensive coordinator for the Baltimore Ravens (2002-2004). That was a job title Nolan held for 11 seasons in the NFL prior to his West Coast arrival. 

The 49ers would be his first endeavor to lead a franchise as a head coach. Nolan also brought his linebackers coach, Mike Singletary, to directly assist him in the Bay Area. This ex-Baltimore staff worked with the early-2000 Ravens, a team that was not far removed from a Super Bowl victory. 

The duo came over as a package deal, bringing a defensive-minded approach to what had long been recognized as a finesse team. From the get-go, Nolan and Singletary were about discipline; they were hard on the players, sought immediate results and left no margin for error.

As if it happened overnight, Nolan transformed San Francisco’s base of operation into Fort Bragg. This militant approach may have worked for thick-skinned defenders that responded to hard coaching, but it was not a universal language accepted by all players, particularly on the offensive side of the ball.

In Nolan’s debut season in ’05, the 49ers finished with a negative-189 point differential, which was second-worst in franchise history. Their disconcerting 4-12 record also placed them near the bottom of the league once again. 

Coach Mike Singletary tears into QB Troy Smith after a mistake on the field.

In three-and-a-half seasons as the head coach—his only in the NFL—Nolan could only muster a bleak .327 winning percentage (18-37). In two of his three full seasons, the 49ers ranked dead last in the league on offense.

Heading into his fourth run in 2008, the team dramatically tumbled to 2-5 before the coach was dismissed midseason. As a quick fix, Nolan was superseded by Singletary in the interim. This change subsequently led to San Francisco’s finest season during that marred time span.

In Singletary’s first full campaign as head coach (2009), the Niners ranked 18th in points for and fourth in points against. At this juncture, the defense was beginning to spark some interest. That breakthrough (an 8-8 record) was the best finish by the organization since 2002.

Seeing as how the 49ers had not won eight games since Steve Mariucci was in town, the mark was considered an improvement. This, in turn, earned Singletary another season on the 49ers sidelines—wooden cross, stopwatch and all. 

However, owner Jed York announcing him as the head coach in the locker room after a Week 17 win over the Rams (1-15) was very reactionary by the young owner. But like his uncle Eddie DeBartolo Jr. before him, this was part of the trial-and-error process. 

In Singletary’s follow-up season in 2010, things had reverted to a ghastly dictatorship, which had largely defined the 2000-decade 49ers team. He failed to open a dialogue, and he continually found himself trying to force a square peg through a round hole.

Rather than converse with his team, he shouted at them. Instead of instructing players, he benched them. It thwarted growth, and it was not hard for the average fan to see that it was an obsolete method. 

His old-school nature was no longer an efficient way to reach players; in fact, it was downright primitive. Singletary’s blood-boiling, hot-under-the-collar tactics personified him as one of the worst communicators in sports. 

It did not take long for his impending release, followed by the 49ers hitting the reset button once again. 

From 2005-2010, San Francisco accrued a 37-59 record, and not once did it surpass the .500 mark in a single season. This botched defensive experiment provisionally sank the 49ers for the better part of a decade.  

 

2. The Predicament Behind Center

49ers pass on Aaron Rodgers in 2005.

In 2005, the 49ers were coming off a tragic 2-14 season, but lo and behold, they possessed the No. 1 overall pick in the draft. This afforded quite a luxury to a fresh staff, enabling them to start anew in the Bay Area...if the front office could only make the right choice at Radio City. 

At the time, Mike Nolan inherited a lackluster roster that was particularly uninspiring at the quarterback position, carrying only Tim Rattay, Ken Dorsey and Cody Pickett. To kick off a new era in 49ers football, the organization was destined to select a new signal-caller. 

According to Matt Miller of NFL Draft Scout, the No. 1- and 2-rated passers that declared in 2005 were Alex Smith (Utah) and Aaron Rodgers (California). It was certainly a close race between the NFL hopefuls, with both of them as projected top-five players.  

As fate would have it, Smith—who strictly operated in coach Urban Meyer’s spread offense with the Utes—was the very first player taken off the board. Interestingly enough, it was not because San Fran’s scouting department favored Smith’s talent over the hometown Rodgers.

It was not even because Smith was necessarily a better fit for the offensive system they intended on running. It was later publicized that the decision came down to compatibility between coach and quarterback.

As it turned out, Nolan found the signal-caller from Cal to be overconfident in the interview process, and he consequently deemed Smith the more “coachable” of the two, per Ann Killion of Sports Illustrated. 

Gary Peterson of the Contra Costa Times provided more thorough insight in regard to Nolan’s thought process:

Nolan was no-nonsense, a strong personality who didn’t like to be challenged. He met with both Rodgers and Smith before the draft. He caught a whiff of attitude from Rodgers, and that was that. Smith was chosen based on personality. He is cerebral, introspective, with a distaste for confrontation.

In short, Nolan felt strongly that he could not coexist with Rodgers, who brought his own individuality to the game. With that being the case, SF selected Smith first overall by default (the 49ers sure were not going to take Charlie Frye or Jason Campbell).

This was not an ideal way to begin either of their careers in the Bay Area. In the public eye, the selection of Smith was meant to be cathartic, but in actuality it was tainted by Nolan's intentions and lack of offensive know-how.  

For the first six years of Smith’s pro career, the quarterback endured shoulder injuries, unrelenting media scrutiny and a half-dozen offensive coordinators. All the while, he had a rotten relationship with two of his head coaches, who showed no faith in him whatsoever.

Instead of investing time and resources in Smith, the 49ers panhandled for quarterbacks to take over for No. 11, bringing in players like J.T. O’Sullivan, Trent Dilfer, David Carr, Shaun Hill, Chris Weinke, Troy Smith and Nate Davis. 

Echoing the sentiments of longtime draft guru Mel Kiper Jr., Gary Peterson wrote that Smith “failed the 49ers as badly as they failed him.” It was a professional partnership that was ill-fated from the very beginning. 

“Imagine Rodgers with the Niners? It could have been the perfect marriage…He was right nearby in Berkeley, and he likely changes everything for the 49ers,” wrote Mel Kiper Jr. of ESPN (subscription required). 

 

3. The Scope of the Team

Average rank for total offense (2005-10): 27.3/32

Average rank for total defense (2005-10): 20.6/32 

The fact that San Fran had no capable receivers and an abysmal secondary is what largely characterized its performances on game day. The team could not stop the pass nor move the ball through the air on a consistent basis.

For the majority of the 2000 decade, the Niners were a perennial loser and the laughingstock of the NFL. Time and time again, the squad found itself at the butt end of ESPN’s "Not Top 10" highlights. 

If pro football counted errors akin to baseball, there is little doubt that San Francisco would have been atop the category. The blown assignments, turnovers and missed coverages were always prevalent, underlining their ineptitude as a team.    

 The 49ers' Achilles (2005-10)
Year Passing Offense Passing Defense Point Differential
2005 32nd 32nd -189 (32nd)
2006 26th 26th -114 (29th)
2007 32nd 25th -145 (29th)
2008 23rd 13th -42 (23rd)
2009 27th 15th 49 (13th)
2010 24th 13th -41 (20th)

Like the 2008 Lions or 2012 Chiefs, the despondent Niners were chalked up as an automatic W on opponents' schedules. This was perhaps the most demoralizing aspect of the team—that the expectation to win had become a thing of the past. 

As a result, that monotonous approach ultimately snowballed and bred more losing. Moreover, given that San Francisco had no direction on the sidelines, it was even more daunting for the team to cultivate leadership on the field. It was a group of 53 individuals, rather than a team, which Mike Singletary emphatically pointed out once or twice.

The tyrannical coaches shouted to high heaven, pining for team-first players, which ironically resulted in further separation in the locker room. This negative reinforcement created a wedge, hindering any progress that might have been made by the players and team as a whole.

To take from the Niners' Bay Area rivals, San Francisco had become a black hole.

There were several players that washed out, either because of lack of talent, a flawed mindset or improper utilization of their skill set. From first-round picks to esteemed free agents, no one thrived in this corrupted environment that was founded on a defective ideology.

Nolan and Singletary wanted "winners” but had no plan on how to achieve that. Their dictatorship tore any semblance of a team apart, and it resulted in the nosedive of both of their careers as head coaches.

So, what does all of this losing have to do with today’s reigning conference champions?

 

The Anomaly That Bred the League’s Most Stacked Roster

49ers consecutive losing seasons results in several high draft picks.

2005: Frank Gore (No. 65)

2006: Vernon Davis (No. 6), Parys Haralson (No. 140)

2007: Patrick Willis (No. 11), Joe Staley (No. 28), Ray McDonald (No. 97), Tarell Brown (No. 147)

2008: Miss

2009: Michael Crabtree (No. 10)

2010: Anthony Davis (No. 11), Mike Iupati (No. 17), NaVorro Bowman (No. 91), Anthony Dixon (No. 173), Kyle Williams (No. 206)

2011: Aldon Smith (No. 7), Colin Kaepernick (No. 36), Chris Culliver (No. 80), Kendall Hunter (No. 115), Bruce Miller (No. 211)

Other notable pros omitted are Alex Smith, Adam Snyder, Delanie Walker, Dashon Goldson, Larry Grant, Ricky Jean-Francois, Taylor Mays and Manny Lawson. 

In accordance with the league’s design, teams that finish with the worst records have the highest pick in the following draft.

This chaotic seven-year run (2004-2010) resulted in several high first-rounders for San Fran. From 2005 until Jim Harbaugh’s arrival, the 49ers either had a top-10 overall pick or a pair of first-rounders six times. 

That is game-changing draft capital.

Though, naturally, the level of ineptitude perpetuates a losing culture (see: Cleveland, Oakland). However, the 49ers did not necessarily do a poor job of recruiting talent, they just failed to properly utilize it on the field. 

As one of the league’s best-kept secrets, the 49ers front office kicked into gear in ‘05, laying the foundation for this team half a decade ago. Going by San Fran’s projected 2013 roster, this seven-year haul netted them seven Pro Bowlers and 12 starters (not including injured Michael Crabtree, Parys Haralson and Chris Culliver).

And all the Niners had to do was lose 73 of a possible 112 games from 2004-2010. 

Coincidentally, in 2005, the same year Nolan and Singletary were hired, San Francisco contracted a man named Trent Baalke to be its western region scout. Partnered with then-GM Scot McCloughan, this sparked a change in the way the team evaluated and acquired college talent. 

The 49ers became intrigued by high-character players, as well as ones that had faced adversity.

A trend began where the team managed to find immensely talented prospects that were overlooked due to imperfect scouting systems. The Niners identified individuals that led their team at the college level but fell on draft day. 

Whether it was character concerns, injuries or listed position, the 49ers snagged certain players earlier than they should have. 

Eliot J. Schechter/Getty Images
Running back Frank Gore tears it up with the Four Horsemen of Miami.

Due to their positions and/or inexperience, tight end Vernon Davis (No. 6), inside linebacker Patrick Willis (No. 11), right tackle Anthony Davis (No. 11), left guard Mike Iupati (No. 17) and outside linebacker Aldon Smith (No. 7) were all first-rounders—and current starters—that San Fran was thought to have picked a bit early.

And in a few cases, they committed utter larceny by taking a player that fell too far. Frank Gore (knee) and Michael Crabtree (foot) are two notables that dropped due to injury concerns. 

Starters NaVorro Bowman, Alex Boone (UDFA), Ahmad Brooks (waivers) and Tarell Brown also hailed from troubled backgrounds. However, the Niners followed their careers, believed in their talent and committed to their development. 

Ergo, not only were the 49ers originally slotted to make promising selections, but they went above and beyond to procure higher-level talent. To this day, it is a risk/reward philosophy that has paid immense dividends.

San Francisco became a safe haven for outcast players with high ceilings. And for the Niners, who had nothing to lose, players that had gone through adverse situations were appealing because they were hardened by circumstance. 

In hindsight, this was brilliant because whoever was coming to the Bay Area was going to have to acclimate to a difficult situation. The team needed players with a callus, particularly ones who would not wilt under intense conditions.

This was not a cushy situation, like being drafted to Bill Belichick’s Patriots or Mike McCarthy’s Packers. 

This went on for years, too, as Baalke climbed the ranks in the San Francisco front office, quietly building one of the most elite rosters in the National Football League. He brought in football guys who simply loved to strap on pads and hit. From 2005-2011, the 49ers drafted 13 of 22 current starters and have seen several others leave for prominent roles elsewhere.

But for years, it was nothing more than nesting talent and unrealized potential. 

All the while, Baalke kept a balanced infrastructure in mind during the process, finding playmakers, an impact offensive line and a league-leading defense. For the most part, the talent was all in place. The 49ers just needed to lock down that final component to tie it all together: a head coach.

 

The Perfect Marriage: Jim Harbaugh and Trent Baalke

Ezra Shaw/Getty Images

Note: As an honorable mention, former GM Scot McCloughan was a major contributor to the current San Francisco 49ers roster, helping piece it together from 2005-2010.

As noted, the under-the-radar hiring of Trent Baalke was the catalyst that set this franchise on the right course. Moreover, kudos to president and chief executive officer Jed York for both noticing and rewarding such a promising individual, especially when several others let him fall through the cracks.

The 49ers were not Baalke’s first NFL stop.

As a regional scout formerly of the New York Jets and Washington Redskins, Baalke has since climbed the ranks, making a home for himself in the Bay Area. By 2008, he had become the director of player personnel, followed by another promotion to the VP of player personnel two years later.

In these roles, Baalke was tasked with oversight for college scouting, which is largely how this roster came to be. His unique criteria for drafting players gave this team an identity San Francisco could be proud of.

In a lockout year in 2011, Baalke was appointed general manager, taking over for McCloughan, who agreed to part ways. During the process, Baalke bested former Raiders and current Browns GM Michael Lombardi as the front-runner for the job, per Mike Sando of ESPN. 

For Baalke, who was bumped up from his recent post, job No. 1 was to find a new head coach:

I would like to thank Jed York and the York family for this tremendous opportunity. It is an honor to be named the general manager of the San Francisco 49ers, a franchise with a history filled by some of the game's greatest players, coaches and executives. I look at this role as one of great responsibility -- to not only the history of the franchise, but also to the 49ers faithful. My entire focus is now dedicated to finding the next head coach of the 49ers.

For fairly obvious reasons, the Niners wanted to stray from defensive-minded coaches, which had failed the organization. And let’s not forget, with the personnel Baalke was assembling, the defense was beginning to play strong football on its own. 

The induction of Patrick Willis and Justin Smith in back-to-back seasons (2007-08) revamped this unit and gave it teeth. Meanwhile, Dashon Goldson was as an All-Pro in the making. However, the offense was still very much in shambles and in need of a rebirth.

Outside of Pro Bowl running back Frank Gore, the 49ers offense was a sad, sad sight.

Roughly 40 miles south of San Francisco, in Palo Alto, there happened to be the hottest coaching candidate in the nation. Stanford head coach Jim Harbaugh, fresh off a prevailing Orange Bowl victory over Virginia Tech, was looking for his next challenge.  

Harbaugh had been making a ruckus in California since 2004, restoring the Toreros (University of San Diego) and Cardinal football programs. He was also the polar opposite of what the 49ers had prior: a player’s coach with an offensive agenda. 

As an added bonus, Harbaugh was a stud when it came to developing quarterbacks, which had long plagued this ballclub.

At the University of San Diego, Harbaugh went 29-6 from 2004-2006 while grooming one of the most exciting passers in the Pioneer League, Josh Johnson. In 2007, the coach took over a 1-11 Stanford team and miraculously turned it into an NCAA juggernaut.

His track record was as flawless as one could hope for.

After being aggressively courted by the 49ers and Dolphins, Harbaugh had accepted substantially less money to remain in Northern California, per Kevin Lynch of the San Francisco Chronicle.

Now, two years and a pair of division titles later, coaches, owners and general managers around the league are realizing this front-office pairing in the Bay Area is an unmitigated nightmare.

Jim Harbaugh introduced as the 49ers head coach in 2011: “It's the perfect competitive opportunity.”

The combo of general manager Trent Baalke and head coach Jim Harbaugh has profound upside for the future. It is a perfect match, through and through.

“I met this man six or seven years ago at a college All-Star game and I fell in love with his energy,” said Baalke, per Mike Sando of ESPN. “This is the start of a new generation. What we have to do is bring back the culture of winning. He's a guy who can lead the 49ers franchise back to where it rightfully belongs.”

This duo, united with the talent in place, was the trigger that catapulted this team into what may be dynastic standing. In these two individuals, the 49ers have one of the nation’s best talent evaluators and one of its best optimizers working in unison.

Together, they also remodeled the coaching staff.

Harbaugh brought in his handpicked crew, which had apparently been on standby, awaiting his inevitable NFL decision. Stanford coordinators Greg Roman and Vic Fangio came aboard, grabbed the reins of the offense and defense, and helped propel this team into a perennial contender. 

In any sport, it is extraordinarily rare to witness a transformation of this magnitude, especially in such a brief period of time.

However, Baalke was a winner and Harbaugh was a winner, and when their paths conjoined, the light turned on in San Francisco. There was just one final step that had to be taken to bring this team to life: find a quarterback of the future. 

 

The 2011 NFL Draft

In Jim Harbaugh's first draft, the San Francisco 49ers trade up to No. 36 overall for QB Colin Kaepernick.

In its most recent and influential draft, the ‘Niners landed a franchise passer and a premier sack specialist. But for the sake of this article (and due to the importance of the position), we’re going to discuss the quarterback that Baalke partnered with his coach of the future.   

As mentioned prior, the 49ers new head coach was a bit of a QB guru, having closely worked with Josh Johnson (Bengals) and the revered Andrew Luck (Colts) during critical developmental years in college. 

This characteristic has given him immense value as a head coach.

Formerly known as Captain Comeback, Harbaugh was a 14-year pro in the NFL (1987-2000). He quarterbacked the Bears, Colts, Ravens and Chargers, even earning Pro Bowl recognition on one occasion.

Considering his firsthand experience, Harbaugh has been able to both relate to players and educate them from a fundamental standpoint. This niche carried over into the NFL, successfully, when the coach revitalized Alex Smith’s career.

In one-and-a-half seasons with Harbaugh, the former No. 1 overall pick threw 35 touchdowns to just 10 interceptions. Overall, the team was playing a more proficient style of football, which enabled the new-look 49ers to go 20-6 with Smith as the quarterback.

This was inconceivable only a few years ago. 

Despite the fortuitous career resurrection, it looks as if Smith was always meant to be the plan for the short term. The 49ers snooped around Peyton Manning, refrained from making any serious monetary commitment to Smith and even drafted a QB early in 2011.

But as Jack Harbaugh, Jim's Father, could attest, the future of the 49ers was always embedded within that particular NFL draft.

The 49ers coach knew he could mold a passer, so he took the highest-ceiling player he could find in Colin Kaepernick—the only individual in NCAA history to throw for 10,000 yards and run for 4,000 yards.

It was production at its finest.

Colin Kaepernick named to the NFL's Top 100.

As a new head coach, Harbaugh felt strongly about Kaepernick, deciding he was the quarterback he wanted to tie his career to. He communicated this to his partner-in-crime, Baalke, who auctioned a second-, third- and fourth-round pick to ensure the 49ers locked up the dual-threat from Nevada-Reno.

The rest is history.

Without question, Kaepernick has surfaced as a league superstar with sky-high potential, and he is still very early in his NFL career. 2013 will be his first full 16-game schedule as a pro starter, which is all the more impressive considering he already has Super Bowl experience.

For a franchise known for its legends behind center—and the uncharacteristically tumultuous years that followed—the 49ers may once again have a very special player at the quarterback position. 

 

Conclusion

Ronald Martinez/Getty Images
Colin Kaepernick is one of the final pieces launching this 49ers team into perennial contention.

First and foremost, if Mike Nolan does not take Alex Smith at No. 1 overall in 2005, there is a high probability the 49ers do not wind up with this pristine roster. The potential selection of Aaron Rodgers would have forever altered history in San Francisco.

This was the decision that set forth a domino effect, ultimately resulting in one of the most talent-laden rosters in the league.

If Rodgers landed in San Francisco and was even two-thirds the player he is now, the 49ers would’ve won more games and had later draft picks. And in all likelihood, high first-rounders like Michael Crabtree, Patrick Willis and Vernon Davis might not be in the Bay Area.

Furthermore, the ‘Niners are probably not in a position to court Jim Harbaugh, who might’ve ended up with the Dolphins after all. The organization also might not be looking for a franchise quarterback, so fans can forget about Colin Kaepernick ever donning scarlet and gold.

Harbaugh might have brought Kap to South Beach, or perhaps he would’ve wound up across the bay in silver and black, like the Raiders intended, via Peter King of Sports Illustrated.

Everything that transpired from 2005 on was very opportunistic and timely, to say the least. It is rare to see that kind of talent successfully stockpiled over that duration of time, as if they were saving it for a rainy day.

At the end of the day, it took Baalke (the architect) and Harbaugh (the engineer) to complete this resurgence; having taken a young talented roster, hardened by failure, and given them a taste of success.

The ‘Niners have since learned to work together and collectively believe in their ability to control the outcome. The coaches have shown them how to prepare while re-instilling the expectation to win, which is half the battle.

It also does not hurt that they are loaded at every position group, which finally includes the most critical spot, the one behind center.

It was awfully serendipitous the way this second chance at a dynasty came about. The San Francisco 49ers and their fanbase had to endure heartache to appreciate what they once had and what they may have again.

This aligning of the stars makes the ‘Niners the team to beat in 2013 and beyond. 

 

 

Dylan DeSimone is the San Francisco 49ers Featured Columnist for Bleacher Report. A former NFL journalist and fantasy football writer for SB Nation, Niners Nation and SB Nation Bay Area, Dylan now writes for B/R.

To talk football with Dylan, follow him on Twitter @DeSimone80

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