Two years later, the three remain on the same page.
San Francisco has just 10 wins over the past two seasons under Shanahan and Lynch's direction. That doesn't mean a drastic change in philosophy will come from anyone in the building.
"We came in here on day one and said our expectations are to be a championship team," Lynch told reporters on Monday. "I think we also said we are not going to put timetables on those things.
"I think what Kyle and I focus on is each and every day making ourselves better, making our organization better by the things we do. We have a philosophy that's rooted in our experiences that when you do that, good things happen. So, we won't put any timetable."
Shanahan already confirmed that defensive coordinator Robert Saleh will return in 2019 despite his unit ranking No. 28 in points allowed and setting NFL record lows for both interceptions and total takeaways. That's proof that Shanahan and Lynch aren't willing to make drastic decisions which deviate from their long-term plan even if a vocal segment of fans wanted to see a change.
Shanahan was asked about the recent communication he had from York regarding the team's progress following the 4-12 season.
"It's been the same since it was when I interviewed with him for five hours (in 2017)," Shanahan said. "That's one of the reasons I wanted to come here. It's talking to ownership and being very blunt and honest about where I personally thought the team was at that time. Hearing Jed's opinions on what he thought, having a plan going into it.
"The stuff that we worked for contractually and things like that, it all had to do with the reality of where we are at or where we were at. We knew it would take some time. That doesn't mean that you're saying, 'Hey, it's going to take four years. Hey, it's going to take three years,' or 'Don't worry, it will only take two years.' That's not at all what you talk about. You talk about the reality of where you are compared to everyone else.
"I think Jed, I, and John, we were very on that same page in the interview process. Everything I think we talked about, we're still on the same page. It's been pretty evident and clear.
"You do have opportunities to do things quicker than you want. Was very excited in our second year that we felt we did find a franchise quarterback, and we thought that could accelerate some of the stuff. Unfortunately, (he) went through a bad injury and that made it tougher."
Both Shanahan and Lynch received six-year contracts in 2017, which keeps them signed through the 2022 season. Time doesn't appear to be an issue yet.
When quarterback Jimmy Garoppolo received his new deal in February valued at up to $137.5 million, it was for five years, which matched the remaining years on Shanahan and Lynch's contracts.
Fans have criticized the 49ers for the team's lack of aggression in pursuing top-tier talent. They were able to land a franchise quarterback in Garoppolo via a trade last year but were unable to pull off a similar blockbuster deal this season. One example is failing to acquire pass rusher Khalil Mack.
While Lynch has stressed that San Francisco's offer for Mack was similar the one that eventually won out, the Oakland Raiders decided to instead deal with the Chicago Bears.
"I hope we never have to make a decision that's based off of because we're going into this year, a third year," Shanahan said. "I hope every decision is we're going to be aggressive because this opportunity came across and we do not want to pass it up; that's what best for this team. That's why I hope something does come up like that and whether it's someone like Khalil, Jimmy, we'll be as aggressive as we can to make that happen.
"But, any time, you're, 'Hey, we have to be aggressive because this is the third year, that's the fourth year,' that's when you're making decisions for the wrong reasons, and that's what can hurt a franchise for more than one year."
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