by Tom Gower

While there was nothing pretty about San Francisco's performance in Week 2 at Seattle, very few fans thought there was much cause for immediate concern. After all, the 49ers had opened the season with a win against a Green Bay squad both our projections and just about everyone else thought would be one of the best in the NFC. The 49ers just had to fly home, lick their wounds, and throttle the Colts, a possibility that did not seem too difficult.

After all, Indianapolis had started the year with close home games against the Dolphins and the likely-woeful Raiders. Their run defense, league-worst by our numbers in 2012, came in ranked 30th and seemed like the cure for a San Francisco run game that had struggled to get going in 2013.

San Francisco's matchup edge seemed further strengthened by Indianapolis' offensive line injuries. Right guard Donald Thomas went to injured reserve last week and starting center Samson Satele missed the game as well. The actual starting interior line for Indianapolis on Sunday was rookie third-round pick Hugh Thornton next to 2012 All-Keep Chopping Wood team contenders Mike McGlynn at center and Jeff Linkenbach at right guard. This seemed like a major matchup advantage for a 49ers front seven that still seems like one of the best in the league.

The story of this game was supposed to be that San Francisco would dominate both lines of scrimmage, throttle the Colts on offense, and walk away with a comfortable win. But the Colts controlled the ball for over 36 minutes in a 27-7 victory, including a 7:01 drive in the fourth quarter that began with 11:14 to play and extended their lead to 20-7. So instead, the story of the game is instead how Colts offensive coordinator Pep Hamilton's preferred power run game helped the Colts control the line of scrimmage and walk away with the win.

By our numbers, the story of the game is somewhat more complicated than that.

By the VOA

The Colts were in fact the better team, but not for a reason anyone I have seen any national outlet discuss.

Some Very Special Teams Team Off. VOA Def. VOA Special Teams VOA Total VOA IND 26.5% -5.8% 9.4% 41.7% SF -0.1% 16.8% -4.0% -20.9%

These are the VOA numbers, not adjusted for quality of opponent, but this is a non-intuitive result. The Colts ran 14 more offensive plays than the 49ers did. The 49ers punted on seven of their eight possessions until the Colts took that two-score lead with just over four minutes to play, including four three-and-outs. Heck, it was even Adam Vinatieri, not Phil Dawson, who missed a field goal in the game. Why are our numbers telling such a counter-intuitive story of what happened?

The Real MVP, and Another Story of What Happened

Here is one attempt at an explanation:

1. P.McAfee kicks 72 yards from IND 35 to SF -7. K.Hunter to SF 13 for 20 yards (M.Harvey).

2. P.McAfee punts 52 yards to SF 9, Center-M.Overton, downed by IND-M.Harvey.

3. P.McAfee punts 51 yards to SF 36, Center-M.Overton. K.Williams to 50 for 14 yards (C.Johnson).

4. P.McAfee punts 46 yards to SF 8, Center-M.Overton, fair catch by K.Williams.

5. P.McAfee kicks 65 yards from IND 35 to end zone, Touchback.

6. P.McAfee punts 43 yards to SF 8, Center-M.Overton, fair catch by K.Williams.

7. P.McAfee kicks 65 yards from IND 35 to end zone, Touchback.

8. P.McAfee kicks 65 yards from IND 35 to end zone, Touchback

9. P.McAfee kicks 63 yards from IND 35 to SF 2. K.Hunter to SF 11 for 9 yards (G.Whalen).

10. P.McAfee kicks 60 yards from IND 35 to SF 5. Q.Patton to SF 12 for 7 yards (S.Havili).

Outside of the punt where Kyle Williams got a return off and the drive (not listed above) that started at their 41 after Vinatieri's field goal miss, Pat McAfee's superb performance meant the 49ers had to go at least 80 yards to the end zone every time they had the ball on offense. Even modestly successful drives ended short of field goal territory, unlike those that start from more advanced field position. Both the Colts and 49ers had drives that gained 35 yards on offense. San Francisco's began at their own 20 and ended with a punt. Indianapolis' began at their own 45 after the 49ers punted from deep in their own territory and ended with a field goal.

One other factor that has not been disseminated in most major stories of the game is penalties. San Francisco was flagged six times, five on possessions that ended in Colts scores. They included two drive-extending defensive holding penalties on third-down incompletions, pass interference on second-and-9, and an unnecessary roughness call that led Donte Whitner to declare that any big hit is now a foul. Whitner had a point, as his hit was not as bad as it looked. The other calls appeared more legitimate. As we have written many times at Football Outsiders, though, defensive penalties like holding and pass interference are generally the result of a healthy level of aggressiveness rather than inherent signs that something is wrong. No call from Sunday's game exemplifies this more than the third-down defensive holding penalty that extended the long fourth-quarter drive: A very close call announced on no specific player. Without it, the 49ers get the ball back with over seven minutes to play down one score instead of with four minutes to play down two scores. The 49ers defense seemed unlucky more than bad on Sunday.

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Offensively, the 49ers actually ran the ball effectively, posting a 14.4% VOA. Frank Gore gained 82 yards on 11 carries, seven of them successful. Kendall Hunter was less effective outside of his touchdown run, but the 49ers did manage to run the ball. It was the passing game where San Francisco struggled for the second week in a row, and where the most serious problems appear to be.

This is no surprise, as with Vernon Davis joining Michael Crabtree and Mario Manningham not in uniform, San Francisco was missing three of their top four targets in the passing game. While Colin Kaepernick has tremendous potential, Sunday was only his thirteenth NFL start and he remains a work in progress as a top-level quarterback. Without the benefit of the all-22 (not yet posted as I write this), it is impossible to tell if his apparent uncertainty in the pocket was a result of receivers like Kyle Williams (two catches on six targets for 12 yards) struggling to find the soft spots in zone coverage or Kaepernick struggling to identify them.

Whichever the cause, the result was the same: San Francisco did not make enough plays in the passing game. Davis was reportedly a true game-time decision on Sunday and should return for Thursday night's contest against St. Louis. That will help, as should facing a St. Louis secondary that has allowed Matt Ryan and Tony Romo to finish fifth in DYAR among quarterbacks each of the past two weeks. Unless and until both Manningham and, particularly, Crabtree return healthy, San Francisco's passing game seems likely to hover close to average, fluctuating between strong and weak performances. That means they need to build on the strength they showed in the run game against the Colts. The return of Davis and his excellent blocking should help here as well.

Three Other Things

1. After Andrew Luck scored on a scramble with 4:13 to play to give the Colts a 19-7 lead, head coach Chuck Pagano elected to kick the extra point rather than going for two for a 14-point lead. It is difficult to overstate just how bad a decision this was. Interpolating Football Commentary's go-for-it chart, the Colts should have gone for two if they had as little as a six percent chance of converting. Obviously the error did not end up costing the Colts anything, but bad process is still bad process.

2. A full exegesis of the Trent Richardson trade is beyond the scope of this column, particularly given his limited impact in the game (13 carries, 35 yards, a touchdown on a second-and-goal from the 1 carry). He had 2 YAR on a DVOA of -3.9% (remember 0% DVOA is average, while the YAR baseline is the lower replacement level). Ahmad Bradshaw looked like the more effective Colts back.

3. Aldon Smith obviously played on Sunday, but both his absence and the groin injury Patrick Willis sustained in the third quarter, one of currently undisclosed and perhaps unknown severity, are serious concerns going forward. My general take on Smith is that, as J.J. Cooper broke down during last year's postseason, so many of his sacks last year came off combination play that his production will be easier to replace than that of a normal 19.5-sack rusher unless Justin Smith has hit the wall at age 33 (34 come Monday). This is, however, the first time in Jim Harbaugh's tenure as head coach the 49ers have faced multiple significant injuries on defense, as they ranked in the top two in Defensive AGL the past two seasons. We will now find how just how much quality development San Francisco has managed behind the scenes. This has been a hallmark of defenses like the Steelers and Bears that have stayed above average for many years and we simply do not know how the 49ers will respond yet.