And now, San Francisco faces an offseason of change with the goal of returning the organization to the upper echelon spot it has held so often in the league's history.
Trent Baalke told KNBR-AM in San Francisco on Sunday afternoon that he has been fired from his position of general manager of the 49ers.
"It didn't surprise me," Baalke said. "We've done some awful good things. Some very successful seasons. Unfortunately regret we weren't able to bring a championship to the Bay Area, which they so deserve. I think The Faithful has been great. Wish this organization nothing but the best moving forward. I do see a bright future for them."
Owner Jed York and the 49ers' key decision-makers are also expected to replace Kelly, multiple sources say. A full house-cleaning is described as "likely" by several people with knowledge of the situation.
"I didn't learn when Trent Baalke was fired," Kelly said. "I was just called (Saturday) night after some of the reports and Jed talked to me and said we would talk today."
When asked about the tone of the conversation, Kelly said "it was a normal conversation."
The 49ers have not had to replace a coach and GM since 2005 when they hired Mike Nolan and Scot McCloughan.
With the move, the 49ers are poised to now go one-and-done with their coach two years in a row. It means they will owe more than $30 million in coaches salaries. But as one source explains, that's not as important as building a winning franchise again.
York told local reporters he'll address them when the season ends. By that time, he'll be ready to sit down and discuss a search for two new faces of his team.