The Niners won on the field, yet lost a highly successful coach as the team and Jim Harbaugh parted ways after four maniacal seasons that had them in three straight NFC title games and a Super Bowl before this year's 8-8 finish.
Indeed, there was apprehension and skepticism sprinkled into the morass.
Quarterback Colin Kaepernick, especially, has a lot to think about, what with Harbaugh making him his hand-picked quarterback after established starter Alex Smith was sidelined with a concussion in 2012.
"He has been a huge part [of my career]," Kaepernick said. "But I'm playing football regardless and quarterback for the San Francisco 49ers, until they tell me different. I'm going to keep truckin' on, be looking forward to find out who they're going to bring in and what we're going to be working on. As far as me, I'm going to continue to work.
"I love Coach Harbaugh and I support him."
Asked if he would become a fan of Michigan, Kaepernick smiled.
"I'll always be a fan of Coach Harbaugh," he said. "Not too sure about Michigan."
Running back Frank Gore, who will become an unrestricted free agent after 10 seasons with the Niners, said he respected both Harbaugh and CEO Jed York, but the inference was that he did not understand the decision.
"I liked how he approached the game of football," Gore said of Harbaugh. "My best years, they were with him. … He was here and we won. I just wish him the best. I know whatever team he goes to, whether it's NFL or college, he's going to be fine. He's going to get it done.
"I respect him a whole lot and wanted to finish it right for him."
Gore had his four young sons with him on the podium. Somebody asked if Harbaugh was already recruiting them.
"If he goes to Michigan," Gore said with a laugh before catching himself, "or whatever college, they've got a shot."
Receiver Anquan Boldin said the whole situation was "weird" for him.
"He had a lot to do with me re-signing back to the team," Boldin said. "So, it's definitely weird. For me, it's something that you didn't see coming, especially with what he had done in previous years. I mean, unprecedented, first three years that you go to at least the NFC Championship. So, definitely didn't see that coming."
Boldin also said he had a "connection" with Harbaugh.
"I just liked the way that he goes about his business, the same way that I do," Boldin said. "No-nonsense type guy. Loves to win. Loves to compete. You see it in the way that he comes to work every day. The guy loves the game of football.
"I believe if he still could play he would probably be out there. You can see that."
Said linebacker Michael Wilhoite: "He gave me the opportunity to play at the highest level. He has given me the opportunity to work my way up. I am grateful for him and thankful for him."
Fullback Bruce Miller said the entire team was behind Harbaugh, despite early-season reports that the coach had lost the locker room.
"So appreciative of everything he has done for me, my teammates, the organization," Miller said. "He's top-notch, class act. We appreciate everything he has done and we love him to death.
"Hate that he's leaving, loved playing for him every minute, every day. … Every single man is appreciative of the things that he has done for our team."