Defenses have figured out how to stop 49ers

By Art Spander

SAN FRANCISCO — Jed York gave the straightforward answer. Jed York, who doesn’t draw up game plans or carry the ball, but in effect as 49ers team president carries the responsibility of having everything done properly, explained what would be done about Aldon Smith.
  
Neither head coach Jim Harbaugh nor quarterback Colin Kaepernick could be, or would be, as forthright, about another problem: the way the Niners have been playing football.
    
San Francisco lost another on Sunday, this time at Candlestick Park, where the crowd of 69,732 appeared more bewildered than irate. Maybe the 29-3 defeat at Seattle a week ago could be understood. But not getting beat, 27-7, by the Indianapolis Colts at home.
   
Two losses in a row for the first time in Harbaugh’s two-plus seasons as the Niners' coach. Offensive ineffectiveness for a second consecutive week. An indication that defensive coordinators around the NFL have figured out how to stop the read-option and thus stop Kaepernick, who was sacked three times, fumbled once and was intercepted once.
    
It’s been a rotten few days for the Niners, who last season went to the Super Bowl. First the whipping by Seattle. Then, early Friday morning, around 7 a.m., the arrest of Smith, the defensive end, on charges of DUI and possession of marijuana. Management decided he would play Sunday — a doubtful decision — and he did play.
   
The defense was satisfactory, to a point, although it never really could stop second-year quarterback Andrew Luck, who Harbaugh coached at Stanford. The offense, outgained 336 yards to 254, was unsatisfactory, out of synch, worrisome.
   
Smith is headed to a rehab center after his fourth arrest and maybe a fine and suspension by the NFL. He won’t be in uniform Thursday when in this loony-tunes schedule, the Niners, 1-2, will play at St. Louis. Some thought he shouldn’t have been in uniform Sunday.
  
There was an apology from Smith after the game, with the comment, “I also wanted to let it be known that this is a problem, and it’s something that I will get fixed, and that I’ll do everything in my power to make sure that this never happens again.”
  
York said Niners executives, realizing there could be outrage from beyond, still “decided that sitting someone down and paying him didn’t seem like appropriate punishment.” As if playing him and paying him is?
   
The Niners, players and coaches, contended that they were not distracted by the Smith situation. That wasn’t the reason they lost, said the chorus. This leaves only one accounting. They were outplayed once more.
   
Kaepernick was brilliant most of the time last year as a mid-season starter. The flaws, maybe a failure to call an audible, perhaps a pass flung too hard, were acceptable. He could run. He could throw, and opponents — with the exceptions of Seattle and, in the Super Bowl, Baltimore — didn’t know how to react.
   
Now, after months of scheming, they do. The serve-and-volley game evens out. First, the offense has the advantage. Then, given time, the defensive coaches create their own edge. So the offensive coaches go to the grease board and devise something else.
   
Athletes are only part of the equation, if the major part. When the defense swarms here or drops three men there, the offense may be stymied. The Niner offense certainly has been.
 
“I think they ran a couple of read-options,” said Colts coach Chuck Pagano, “and our guys did an unbelievable job on (those) . . . We talk about plastering so guys don’t come out free on the back end once he starts to scramble. The pass rush was just relentless.”
  
Kaepernick, never very informative, retreated behind the obligatory “it wasn’t them, it was us,” or in his words, “The fact is we didn’t execute.” Why doesn’t anyone ever admit he/they didn’t execute because the other team wouldn’t let them?
  
“They put a spy on me,” Kaepernick said about a defender who follows the quarterback, “so they have one more to account for me. I have to be able to make throws downfield.”
  
Not an easy task when under ferocious pressure.
 
Harbaugh said he didn’t believe there was something technically wrong with Kaepernick.
   
“We didn’t make the plays,” said Harbaugh, sticking to the format.
    
Then a bit of honesty snuck in: “There wasn’t enough opportunity to make plays.”
    
Because of the Indianapolis defense. Because perhaps the Niners were without their best receiver, Vernon Davis, and already had lost another receiving star, Michael Crabtree, on an injury before the season began. Still, every team has injuries. The best overcome them.
 
“We got to be real,” said Harbaugh, “got to look how we can improve. We have no choice but to find our way.”
  
No choice except losing games.