Jimmy Garoppolo will be the No. 2 quarterbacks in the 49ers’ regular-season opener

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Jimmy Garoppolo will make $6.5 million this year. He’ll get another $29,000 next weekend.

During a Tuesday press conference, coach Kyle Shanahan told reporters that Garoppolo will be the No. 2 quarterbacks when the 49ers visit the Bears in Week One.

It’s a stunning turn of events. GM John Lynch was asked to explain how Garoppolo went from inevitably being off the team to being on it.

“Kyle and I always talk about the direction of our team and this situation with Jimmy has been going on for some time,” Lynch said. “I think we’ve been consistent with a player of his caliber, you don’t just allow him to walk and then complicate other things as we’ve talked about a lot with his shoulder surgery. And so that never materialized, obviously there were going to be some deadlines, but Kyle and I just started floating the idea probably a month ago. What if we kept them here in a backup capacity and at some point, we shared that with Jimmy? It was important for Kyle to let Trey [Lance] know that that may be a possibility. And I think that was the right thing to do, but the crux of the matter is that this wasn’t going to happen. And I understand it completely from Jimmy’s side, he had his current contract and they were going to exhaust every opportunity. His agents, Carter Chow and Don Yee, have been doing this for a long time and probably rightly so. I remember at one conversation, think if this were your son, you’d wait for every opportunity to collect that whole salary. And the way you do that is a lot can happen and so they waited it out. We waited out, but we had been in communication and then, it kind of came to fruition yesterday morning and it was finished slightly after we got off the practice field. That’s the timeline.”

There was still confusion expressed by reporters during the press conference, given that the team had said in clear terms that Garoppolo would not be back. If they were keeping him, why wasn’t he in meetings or at practice?

“I think that was because, the chances were to me it seemed slim to none, just with the possibility of that happening,” Shanahan said. “I told Jimmy, he came in here the first week of training camp, like I told you guys, we would talk. We talked regularly because he was up here, he wasn’t in meetings or practice, but I remember the first week of training camp me saying to Jimmy like, ‘Hey, if you don’t like any of these opportunities, if you don ‘t go to the place you want, you can’t get the contract that you want, we would love to have you here as a backup, in a backup role. I want you to know that we feel that way, but I also think there’s no way you’re not going to get something as this goes throughout training camp.’ And Jimmy agreed with that. And so we waited throughout all training camp and then as I think as he saw the other situations out there and I think, to me, it seems like everyone was just waiting for us to cut him before that so they could see how much they could get him for

‘But once the last Saturday preseason game happened and no one got injured, then Jimmy thought this was his best situation that he liked. And that’s why we were so pumped, because it’s obviously a better situation for the Niners. We love getting Jimmy back, but to have him there earlier in camp wasn’t an option. We weren’t going to put him out there in practice for his sake and for our sake, he was on a $24 million contract and he was going to go somewhere else, but none of that came into fruition, which we would’ve ended up having to let him go under that current deal. That wasn’t an option, but we were always clear to Jimmy that him salary cap-wise in a backup role and supporting Trey in that and if that worked for him, that was a no-brainer for us. We just didn’t think the chances of that were going to happen. And it ended up being that way and so, when it was all said and done, even though it was pretty shocking to us, we thought it was a win-win for both sides.”

It really was a win-win, in large part because Garoppolo decided to go along with the plan and not force the issue in late July. Basically, he bet on an injury happening that would allow him to get something closer to the $25.62 million he was due to earn, instead of forcing his way to the open market by, for example, making a stink about not being allowed to practice and potentially giving the 49ers no option but to cut him early in camp. By late August, his best option became slashing his base salary by more than $19 million to stay put.

As we said yesterday, the 49ers didn’t plan it. But they couldn’t have planned it any better. They’ve kept a fringe top-20 quarterback as the backup Trey Lancewhile they find out whether he’s any better than that.

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