Kaepernick's representatives informed teams earlier this week that he would be opting out of the final year of his contract with the 49ers. The paperwork was finalized and filed Friday. Kaepernick, who restructured his contract last October, will become an unrestricted free agent when the new league year begins next Thursday.
But even if Kaepernick hadn't exercised that option, he wouldn't have been back with the 49ers under the terms of his current contract. General manager John Lynch told SiriusXM radio on Thursday afternoon that the team would have released Kaepernick had he not elected to opt out.
"Kaep is going to opt out," Lynch said. "We had a great conversation with him. We had a great meeting, and I think we had a very frank and honest discussion, and what we both agreed was that under the current construct of the situation, everything, the contract, it wasn't going to work."
The Niners aren't ruling out a reunion with Kaepernick -- "We left that door open in a very real and positive way," Lynch said Thursday at the NFL combine -- because San Francisco will have no quarterbacks under contract for 2017 at the start of the new league year.
A former second-round pick in 2011, Kaepernick had the fifth-best touchdowns-to-interceptions ratio (14 to 3) among all starting quarterbacks during the second half of last season. Kaepernick, who's had three surgeries, is back up to between 225 and 230 pounds. His weight was a subject of interest from personnel executives last season.
Kaepernick joins Blaine Gabbert, Christian Ponder and Thad Lewis as 49ers quarterbacks set to explore the free-agent market. Because of that, Lynch and coach Kyle Shanahan acknowledge that finding help for the game's most important position is the top priority.
"We are looking at every option," Lynch told Sirius. "We need to. Free agency, there's some viable options there. I'm excited about this draft class. I think a lot of people have criticized these guys. As I watch them, I get excited. I think with the No. 2 pick in the draft, that's a valuable asset, and it gives us a lot of options at our disposal. One thing Kyle and I have talked about: When you have no quarterbacks, it's not an ideal situation, but what it does, it allows us to go get people.
"Obviously there's constraints, but it allows us to form it in the way we want. We aren't taking other people's stuff that maybe we aren't thrilled about. We can go say, 'Hey, these are the guys we want to play with.'"
One option is pursuing Washington Redskins quarterback Kirk Cousins. Washington placed the exclusive franchise tag on Cousins this week, effectively denying him the opportunity to even negotiate with other teams. That means that if the Redskins decide to part with Cousins, it will come via trade -- and with a presumably hefty price.
Lynch said Thursday he has not had any discussions with the Redskins about Cousins, but he did say he has great respect for the veteran and reiterated, "All options are available to us."
Earlier on Thursday, Lynch spoke highly of some of the top quarterbacks in this year's draft class. The Niners interviewed Notre Dame's DeShone Kizer on Wednesday night at the combine in Indianapolis, and Lynch said Kizer "blew the doors off" the room with an impressive performance.
During his media session at the scouting combine on Wednesday, Shanahan said he hadn't yet had a chance to dive into the top of the college prospects, but he offered some insight into what he's looking for at quarterback.
"Really, how quick they process things," Shanahan said. "You can tell [by] talking to people who's capable of processing a lot, but the smartest people aren't always the best quarterbacks either. You can overprocess things. So, it's how quick they react in the pocket. Do they watch the rush? Are they fearless? If they're watching the rush at all and things like that, it's very hard to make the reactions you need to make in this league with how quick these windows close.
"So you want to see how quick their decision-making is. Not on the board, but in the pocket when they're under duress."
No matter the avenue, the Niners will add multiple quarterbacks over the next couple of months. It's just a matter of how they go about doing it.
"We understand how critical that position is," Lynch told Sirius, "and sometimes you have to be bold to secure a guy that you think is a franchise guy. And we're both willing to do that, and there's a number of different ways that we can and we're exploring all those options right now."