Grant Cohn: Chip Kelly's version of 49ers' Colin Kaepernick's fall is fantasy, not fact

For his first trick as head coach of the San Francisco 49ers, Chip Kelly tried to rewrite history.

He did this Wednesday morning at the NFL owners’ meetings in Boca Raton, Fla., did this in front a group of reporters. One had asked Kelly why Colin Kaepernick played so poorly last season. Get a load of Kelly’s response:

“I think the biggest misconception that people don’t realize with Kap is just injuries. It’s not like his skill set diminished. He went on injured reserve last year. He only played half a season. He was legitimately injured. He’s in the process of rehabbing right now. He had a thumb, had a shoulder, had a knee.

“People look at it as he fell off. He didn’t fall off. He got hurt. I think the biggest thing with Kap is let’s get him healthy. I think the league has seen a healthy Kap and he’s pretty impressive.”

First of all, kudos to Chip for trying such a difficult trick. Rewriting history isn’t easy, especially when the rewriter was 3,000 miles away from the events when they happened. Kelly lived in Philly last season. He had his own problems to deal with, problems he couldn’t solve. And, while he tried to deal with those, we’re supposed to believe he simultaneously made himself a Kaepernick expert.

Of course, Kelly is no Kaepernick expert. Kelly is a secondary source whose story sounds like hearsay. Incorrect hearsay. Hearsay that directly contradicts what we know to be true, and what Niners general manager Trent Baalke said after the team placed Kaepernick on injured reserve last season. Baalke was in Seattle before a game against the Seahawks when a reporter asked him if Kaepernick’s injury had anything to do with him getting benched. “No,” Baalke said.

Baalke should know the real story of why Kaepernick lost his job. For Chip’s sake, let’s review what actually happened.

Week 1. The Niners beat the Minnesota Vikings, a team that would go on to make the playoffs. Kaepernick wasn’t great in this game - he threw no touchdown passes and gained only 165 yards through the air - but he outplayed Vikings quarterback Teddy Bridgewater, and suffered no injuries. Kaepernick seemed on the verge of a good season.

Week 2. The Niners got crushed by the Pittsburgh Steelers, but Kaepernick played well in the second half when the game was out of reach. He also suffered no injuries. He looked like a pocket passer in this game, completing 71.7 percent of his attempts and throwing for 335 yards and two touchdowns. Some of us thought Kaepernick finally had become the quarterback we always thought he could become.

Week 3. A few days before the Niners played in Arizona, Cardinals safety Tony Jefferson appeared on “Pro Football Talk Live” to preview the matchup. The host of the show, Mike Florio, asked Jefferson what he was seeing from Kaepernick. Jefferson was not impressed. “We’re just seeing on third downs, we’ve been seeing him tuck the ball away and running,” Jefferson said. “We gotta contain him, and try to keep him throwing the ball outside the numbers, because we don’t think that’s his strength.”

On Sunday, Kaepernick responded by throwing pass after pass outside the numbers and toward the sideline. He clearly was trying to prove he could do what Jefferson said he could not. But, Kaepernick threw four picks, including two pick-sixes, all of which came on throws that traveled outside the numbers. Kaepernick singlehandedly lost the game, although he didn’t suffer an injury.

Week 4. Kaepernick was freaked. He knew he might get benched on the spot if he threw another pick-six, so he threw passes almost no one could catch, not even his teammates. Mostly, he threw groundballs. He completed only 13 passes that game, the Green Bay Packers sacked him six times, and Kaepernick suffered an injury to his left shoulder, his non-throwing shoulder.

“It was an injury our medical staff looked at and treated,” Baalke said a few weeks later in Seattle the morning after placing Kaepernick on I.R. “He didn’t seek any extra treatment. It was ongoing … He went in, got checked, felt good and kept playing.”

Week 5. Kaepernick looked like he felt good. He threw for 262 yards and led the offense to 27 points, although the defense gave up 30 and the Niners lost to the New York Giants. Still, Kaepernick had one of his better games of the season. He seemed completely healthy.

Week 6. Niners beat the Baltimore Ravens and, again, Kaepernick seemed completely healthy. He played even better than he did against the Giants. He even outplayed Ravens quarterback Joe Flacco, who beat Kaepernick in the Super Bowl. Kaepernick seemed to be improving.

Week 7. The 2-4 Niners faced the Seahawks, who also were 2-4. The Niners were the home team, and the Seahawks were coming off a Thursday night loss against the Carolina Panthers. The Niners had every advantage. They should have won.

But, they didn’t. The Niners scored just three points, and Kaepernick threw for only 124 yards. He seemed intimidated by the Seahawks. He hardly competed. A couple of days later, reports came out that he had lost the Niners locker room.

Week 8. Niners played in St. Louis, and Kaepernick seemed confused on the field. Seemed like he didn’t study that week for the Rams defense. Completed only 48.8 percent of his passes, took a sack in the end zone and didn’t see uncovered receivers. He looked unconfident and unprepared, but he didn’t look injured.

Week 9. The Niners benched Kaepernick for Blaine Gabbert. And in his first start with the team, Gabbert led the Niners to a victory against the Atlanta Falcons.

Week 11. After a bye week, the Niners chose to give Gabbert one more start, although they didn’t make him the full-time starter. They said they would decide weekly which quarterback they would play. Kaepernick didn’t go for that plan. Instead, he had season-ending-surgery on his non-throwing shoulder, an injury he played through since Week 4.

Kaepernick chose to quit instead of compete with Gabbert. That’s what really happened.

Kaepernick got benched based on merit, not based on injury. He seemed clueless without Jim Harbaugh feeding him answers to the problems opposing defenses presented. Gabbert never seemed clueless - he mostly knew where to throw the ball. According to reports, Gabbert spent about five times longer watching film than Kaepernick, and you could tell.

Kelly doesn’t want to get into any of that. Kelly wants to stroke Kaepernick’s ego, wants to keep Kaepernick on the Niners next season. Kelly simply is saying what Kaepernick wants to hear, even if what Kaepernick wants to hear is historical fiction.

Grant Cohn writes sports columns and the “Inside the 49ers” blog for The Press Democrat’s website. You can reach him at grantcohn@gmail.com.