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The 49ers’ season comes to an end on Sunday. It will signal the end of a fascinating time in 49ers’ history.

Many changes will be made as the 49ers fail to make the playoffs for the first time in coach Jim Harbaugh’s four seasons. Before Harbaugh arrived with the 49ers, the organization struggled through eight non-winning, non-playoff seasons. He helped change that during the past three seasons.

Now, that time is over.

We open up the 49ers Mailbag to find one question that stands out among the others. It’s a broad question, but one that is certainly being asked by many 49ers fans:

In your opinion, what went wrong this year? (John Falabella)
The simple answer is . . . just about everything.

The on-field problems began last season. NaVorro Bowman and Mike Iupati were injured in the NFC Championship game. Bowman was sidelined for the entire 2014 season, taking one of the best players at his position out of the 49ers’ lineup. Iupati sustained a fractured leg, and he did not appear to round into shape until about the mid-point of this season.

Three consecutive playoff appearances and deep runs in the playoffs might have had a cumulative effect on the health of the 49ers – a theory one team official believes has a lot of validity.

After all, not only did the 49ers play eight playoff games the past three seasons. But those games are played at a higher level of mental and physical intensity. It takes an immeasurable toll on the players.

In 2011, the 49ers had just two players placed on injured reserve during the regular season. In 2012 and 2013, the 49ers placed four players on IR in each of those two seasons.

This season, the 49ers have placed 14 players on season-ending injured reserve since the first week of the regular season.

Could it be that the wear-and-tear of playing so many extra high-stakes, intensified games contributed to all of this season’s injuries?

“It could be. It could be a cycle,” coach Jim Harbaugh said. “it could be a lot of different things. I don’t really have anything concrete. Some guys were injured that didn’t play in those three consecutive postseason games as well. So, (it’s) hard to speculate on that one.”

Off the field, it’s also hard to speculate why leaks on the inside, beginning Week 1, to begin exposing some of Harbaugh’s negatives. There were reports of a fractured locker room and dysfunction involving the coach and the team’s ownership and management on nearly a weekly basis.

The distractions became more severe as the losses mounted. Or did the losses mount because of the distractions?

On the field, the defense handled its business despite a rash of injuries. Certainly, the 49ers lacked a lot of the physicality that it had used to intimidate opponents in the past, but the defense remained solid from beginning to end. Remarkably, the 49ers enter the final game of the regular season Sunday against the Arizona Cardinals with the league’s fifth-ranked defense.

The offense, however, was a disappointment.

The offensive line was thought to be the strength of the team. But that unit did not play well. Quarterback Colin Kaepernick did not develop into an effective pocket passer. And offensive coordinator Greg Roman came under fire – most notably from right tackle Anthony Davis this week.

[MAIOCCO: Anthony Davis: 'I just know what we don't need']

The 49ers featured a power-based running game in the past three seasons. But in the offseason, general manager Trent Baalke made it a priority to supply the offense with better weapons on the outside. The 49ers traded for Stevie Johnson to be the No. 3 receiver. He also added Brandon Lloyd and selected Bruce Ellington in the draft.

The signal from upstairs was clear: The 49ers had more depth among their pass-catchers to feature multi-receiver formations. So the 49ers used more spread elements this season than in the past.

Davis suggested the emphasis on power running had powered the 49ers to the playoffs in three consecutive seasons. But he also said the 49ers had more talent on offense than ever. Those upgrades were geared toward the passing game, though.

Davis is one of the team’s best run-blockers. When it was suggested to him that part of the reason the 49ers did not lean more toward the running game – and they were not as successful – was because he was inactive for nine games due to hamstring, knee and concussion issues. He conceded, “It’s possible.”

Ultimately, what happened to the 2014 San Francisco 49ers is that not enough people were pulling in the same direction.

From upstairs to the coaching staff to the team’s two locker rooms, the 49ers had too many individuals with their own agendas.

It was no longer about, “The team, the team, the team,” as Harbaugh preached when he changed the culture of the organization upon his arrival in 2011.