So why didn’t the 49ers’ evaluation of quarterback Peyton Manning become a full-blown pursuit and ultimate acquisition of Peyton Manning?
Per a source with knowledge of the situation, Manning ultimately chose not to make the 49ers a finalist for his services. Apart from Manning preferring to stay in the AFC, the wind and precipitation at Candlestick Park (where Manning would have played for two years) were factors. Another factor was the potential for friction between Manning and coach Jim Harbaugh. According to the source, Manning feared that it would be difficult for a pair of ultra-competitive men to coexist.
In Denver, Manning enjoys a high degree of autonomy on of the offensive side of the ball, especially since coach John Fox worked as a defensive coordinator. In San Francisco, Manning and Harbaugh each would have wanted to run the offense. And they each would have been willing to argue aggressively in support of their ideas and preferences.
Seth Wickersham of ESPN The Magazine recently repeated a story that had made the rounds in 2012 regarding the interactions of Harbaugh and Manning.
“Harbaugh and Manning were throwing the ball, so it goes, when the coach couldn’t help but remark that his passes had more mustard on them than the still-rehabbing future Hall of Famer’s did,” Wickersham wrote. “You can guess how that went over.”
In the end, Manning decided not to go over to the 49ers. Eventually, the finalists were the Broncos, Titans, and Cardinals. Other teams that wanted a seat at the table didn’t get one, including the Seahawks and the Chiefs.
The official story from the 49ers is that they weren’t pursuing Manning at all.
“There’s a perception out there and it’s an erroneous perception that we were flirting with Peyton Manning,” coach Jim Harbaugh said in May 2012, more than two months after Manning picked the Broncos. “I keep hearing it over and over. It’s silly and it’s untrue. It’s phony. Even the perception that we were pursuing. We were evaluating. I’ve said all along that Alex Smith has been our quarterback. There’s no scenario, other than Alex choosing to sign with another team, that we would consider him not as our quarterback.”
Of course, there was another scenario in which the 49ers would consider Alex Smith not their quarterback. It unfolded during the 2012 season after Smith suffered a concussion and Colin Kaepernick emerged. The 49ers then traded Smith to the Chiefs.