What in the heck is going on with the San Francisco 49ers?

From the time Jim Harbaugh and the San Francisco 49ers “mutually” parted ways right after the season ended, two things happened.

Pretty much nobody believed that it was truly “mutual,” and people started wondering what in the heck was going on with the 49ers.

Over the past few days San Jose Mercury News columnist Tim Kawakami, who has been harsh on the 49ers brass of owner Jed York and general manager Trent Baalke, has put that “What in the heck is going on with the 49ers?” question in clearer contest.

To sum up his interview with Harbaugh and a follow-up story, Kawakami writes that the 49ers planned to get rid of Harbaugh for all of 2014, they leaked stories that said he wouldn’t be back in 2015 (those two things seemed fairly clear already), in Kawakami’s words the 49ers brass “torched the 2014 season in the process,” and then botched hiring Adam Gase as Harbaugh’s replacement when at the last minute they told him Jim Tomsula would have to be his defensive coordinator if he wanted the job. Gase refused. Tomsula went from defensive line coach to Harbaugh’s replacement.

It all adds up to a really weird situation (not that replacing one of the best coaches in the NFL for a defensive line coach wasn’t already strange) and a bad way for the 49ers to start off 2015.

First, Harbaugh claimed that he was told with two games left in the season that he wouldn’t be the 49ers coach in 2015.

“I didn’t leave the 49ers. I felt like the 49er hierarchy left me,” was Harbaugh’s money quote to Kawakami.

Mutual? Hmm. The rest of the interview is illuminating. Harbaugh avoids answering questions about where certain leaks during the 2014 season came from but it’s pretty clear he believes they came from within the organization, particularly those about Tomsula being his potential replacement.

“Those are good questions for him and the 49er hierarchy. And we’ll leave it at that,” Harbaugh said.

Then came what happened after Harbaugh was let go. Kawakami said that the 49ers had all but agreed with Gase, then the Denver Broncos offensive coordinator, to be their head coach. They approved his coordinator choices, and Tomsula’s name didn’t come up. Then the next day he was told that Tomsula would have to be his defensive coordinator if he wanted the job. Gase passed. Tomsula was hired. Then, Kawakami wrote, Tomsula asked Gase if he wanted to be his offensive coordinator. That was predictably shot down by Gase, who went to the Chicago Bears to run their offense.

The first three years Harbaugh was the 49ers coach, the franchise went from one of the worst in the NFL to one of the best. They made three straight NFC championship games and came very close to winning a Super Bowl. Last season was a bit of a mess, with an 8-8 finish, and all of the backroom battles as Harbaugh and the 49ers brass clashed is one reason for what happened last season.

The new coaching staff, starting at the top, has a lot to prove. If they can’t replicate the success Harbaugh had, and it won’t be easy to put together a record like 44-19-1 as Harbaugh did, the 49ers will have a lot of questions to answer. The workplace environment with the unpredictable Harbaugh might be calmer with him off to the University of Michigan, but it’s hard to see at this point how the 49ers will be more successful on the field.

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Frank Schwab is the editor of Shutdown Corner on Yahoo Sports. Have a tip? Email him at [email protected] or follow him on Twitter! Follow @YahooSchwab