Big games often come down to a few plays.

The 49ers came up just short in Super Bowl LIV, losing 31-20 to the Kansas City Chiefs at Hard Rock Stadium.

The end of the first half saw one of the game’s most controversial calls, as tight end George Kittle was whistled for offensive pass interference, negating a 42-yard completion that would have set the Niners up in Kansas City territory in ideal position for a field goal.

“Ref made the call, I gotta live with it,” Kittle told reporters following Sunday’s loss at Hard Rock Stadium.

Replays clearly showed Kittle fully extending his right arm and creating separation from the defender, which by definition is a penalty.

The receiver extends his arm and creates separation while the ball is in the air, therefore it is offensive pass interference. – AL#SBLIV pic.twitter.com/hxAvggDqhS

— NFL Officiating (@NFLOfficiating) February 3, 2020

49ers head coach Kyle Shanahan was seeing a lot of contact from both teams in the passing game.

"I don't get to see it very good from the sideline,” Shanahan said. “But I was definitely surprised the way they were letting them play defense."

[RELATED: 49ers blow 10-point lead, lose Super Bowl LIV vs. Chiefs]

Fans claiming the officiating cost San Francisco the game seem to forget that Kyle Shanahan burned almost an entire minute off the clock before deciding to run a two-minute drill, which left the 49ers with almost no time to adjust following the penalty.

This loss will sting for all of the 49ers’ Faithful for years to come, but the blame doesn’t belong anywhere outside of the San Francisco locker room.

The 49ers this season had a unique blend of talent, depth, chemistry and coaching that enabled them to win 15 of 19 games en route to the NFC West championship, the No. 1 seed in the conference and a berth in the Super Bowl.

The 49ers’ season fell short of their dream, as everything fell apart after 3 ½ quarters of Super Bowl LIV on Sunday in Miami Gardens, Florida.

All the phases of the team that came together to enable the 49ers to get tantalizingly close to their sixth Super Bowl title in franchise history disappeared with a blown coverage, the flick of Patrick Mahomes’ wrist, a couple swatted down passes and a potential big play that sailed out of reach.

The 49ers blew a 10-point lead in the final minutes. The Kansas City Chiefs rallied from a 10-pont deficit in the final minutes. Take your pick. It’s all the same.

The 49ers lost, 31-20, to Andy Reid’s team – a team that made more plays at important moments of the NFL’s most-important game of the season.

Tears were shed on the sideline. Tears were shed in the locker room. The 49ers’ season is over, and all we can do is look back and remember.

Here are the final season-long grades from a special season that graded out just shy of super:

Rushing offense

For only the second time in franchise history, the 49ers had three running backs rush for 500 yards apiece in a season. Raheem Mostert, Matt Breida and Tevin Coleman gave the 49ers a solid 1-2-3 punch.

During the playoffs, the 49ers went with Mostert and Coleman. Mostert rushed for 220 yards and four touchdowns in the NFC Championship Game. He had five rushing touchdowns in the playoffs.

Coleman gained 105 yards and two touchdowns in the playoff opener against the Minnesota Vikings. Breida played sparingly late in the season and did not play a snap of offense in the Super Bowl. He gained just 19 yards rushing in the postseason.

The key to the 49ers’ rushing attack was the blocking of the offensive line – Joe Staley, Laken Tomlinson, Ben Garland, Mike Person and Mike McGlinchey – along with tight end George Kittle and the wide receivers.
Grade: A

Passing offense

Jimmy Garoppolo had one of the best statistical seasons for a 49ers quarterback in the past two decades. He threw for 3,978 yards, which ranks fourth for a single season in franchise history.

His 8.4 yards per pass attempt and 102.0 passer rating were very good. He had two of his best games in such difficult environments as New Orleans and Seattle. Garoppolo was somebody the 49ers counted on during the regular season.

In the playoffs, the 49ers’ running game took center stage. Garoppolo was rarely asked to drop back and throw the ball around the field as the 49ers made it out of the NFC side of the bracket with relative ease.

In the Super Bowl, Garoppolo completed 18 of his first 22 pass attempts. But things finished with a thud, as the offense could not string together drives in the fourth quarter.

Although the 49ers had 13 players catch touchdown passes from Garoppolo, their passing game ultimately consisted of just four targets: George Kittle, Deebo Samuel, Emmanuel Sanders and Kendrick Bourne. Although efficient throughout the season, the passing game did not come through in the Super Bowl.
Grade: B

Rushing Defense

The 49ers played with a lead for most of the season, so opponents generally did not stick with the run. That was certainly the case for the 49ers’ first two playoff games. They forced teams to be one dimensional.

The 49ers did a good job of defending the run, and forcing teams into third-down situations. But the 49ers did have some difficulty against Kansas City running back Damien Williams in the Super Bowl. Williams rushed for 104 yards (6.1 average) and a touchdown.

Linebacker Fred Warner did an excellent job from beginning to end as the 49ers’ middle linebacker and top tackler. The defensive line also did a good job of controlling the line of scrimmage to allow the linebackers to roam free and make tackles.
Grade: B-plus

Passing Defense

The 49ers’ pass defense was not only the best in the NFL this season. Their pass defense yielded the fewest yards per game in more than a decade.

It all started with the pass rush. Rookie Nick Bosa led the 49ers in sacks over the course of their 19 games. He had 13 sacks, including four in the postseason, while Arik Armstead registered 12 sacks. DeForest Buckner was also a force, and Dee Ford was productive, when healthy.

The constant pressure took a lot of heat off the defensive backfield. Jimmie Ward and Jaquiski Tartt were solid at the safety positions. Richard Sherman earned a trip to the Pro Bowl. The 49ers had some uncertainty at the other spot, where Emmanuel Moseley eventually took over for Ahkello Witherspoon in the playoffs.

For 3 ½ quarters of the Super Bowl, the 49ers made Mahomes look ordinary. Warner and Tarvarius Moore came up with interceptions, and the 49ers sacked Mahomes four times. But the 49ers left Mahomes enough of an opening late in the game, and he made them pay.

Despite the way this season ended, there’s not much more that can be expected from this group.
Grade: A

Special Teams

After a rough start to the season, Robbie Gould and the place-kicking operation finished strong. Gould, holder Mitch Wishnowsky and long-snapper Kyle Nelson came together to execute some big kicks down the stretch.

So much of the 49ers’ problems early in the season can be traced to Nelson’s suspension and a period of time in which the 49ers cycled through three different long-snappers before Nelson returned to the team.

Wishnowsky was consistent as a rookie punter. His net average was 41.6 yards in the regular season and 41.1 in the playoffs. He was not as good on kickoffs, where did not show the leg strength to regular drive the ball into the end for touchbacks.

Mostert, in addition to being the team’s top rusher, was also the 49ers’ leading tackler on special teams.

Richie James was steady as the punt returner, until he muffed a punt on his first chance in the Super Bowl. He recovered his own fumble to avert a disaster.
Grade: B

[RELATED: Why 49ers' stunning 2019 season will be nearly impossible to replicate]

Overall

The 49ers have some playmakers on offense, but maybe not to the elite level as other teams. Still, they ranked second in the NFL in points (29.9) and fourth in total yards (381.1).

Coach Kyle Shanahan, with big assists from coordinators Mike McDaniel and Mike LaFleur, schemed it up beautifully in the run and passing games. Shanahan proved to be one of the top play-callers in the business. The 49ers’ difficulties in the final quarter of the Super Bowl do not change that.

Defensive coordinator Robert Saleh did a very good job on the other side of the ball with game-planning and adjustments. He got helping hands from a couple of newcomers to his staff: defensive line coach Kris Kocurek and defensive backs coach/passing game coordinator Joe Woods.

Coming off a four-win season, the 49ers greatly exceeded expectations. The sting of squandering a 10-point lead in the fourth quarter of the Super Bowl is still fresh, of course. But all these pieces had to fit into place for the 49ers to advance to Super Bowl LIV in the first place.
Grade: A

There's no shortage of criticism being directed at 49ers coach Kyle Shanahan for San Francisco's stunning collapse against the Kanas City Chiefs in Super Bowl LIV. However, it's not coming from within his own locker room.

Quite the opposite, actually.

The strong bond between players and coaches that was emboldened over the 49ers' progression from the No. 2 overall pick in the draft to NFC champions was readily apparent in the comments emanating from their distraught locker room following the 31-20 loss at Hard Rock Stadium in Miami Gardens. 

After finishing his postgame press conference, Shanahan returned to his deflated team. Surely, he was in a terrible mood as well, knowing that for the second time in four years, he had the Lombardi Trophy in his grasp, only to see it slip away. Nonetheless, he put his personal disappointment aside and, according to NFL Media's Mike Silver, delivered an uplifting speech befitting of a leader. His players certainly appreciated it.

"Kyle held his head high," defensive end Dee Ford described. "He told us, 'Of course it's not the result we wanted, but I'll line up with any player in here, anytime.' He told us, 'This team is special.' And it is."

As sad as tight end George Kittle was while watching his coach have to make that speech -- rather than the joyous one they were all hoping for -- he valued the sentiment of Shanahan's message.

"S--t, it was brutal," Kittle said. "I don't know how to describe it. It just sucked. Kyle was great, though. That's one thing I do like about Kyle is, he keeps it real, all the time. I love playing for him."

Fullback Kyle Juszczyk scored one of San Francisco's two touchdowns in the Super Bowl, and played a critical role in setting up the other. He was one of the first free-agents to sign with the 49ers after Shanahan was hired ahead of the 2017 season, and he had only glowing things to say about his coach after the lowest point of their time together.

"I have so much love and respect for Kyle," Juszczyk said. "He's the best coach that I've ever played for. He's the same guy every single day, no matter what happens. He always looks to himself first when it comes to blame. And he takes our ideas and suggestions and will really listen, and think about implementing things after the fact. It sucks just because of how much everybody respects and loves him, and because we hate to hear any negativity about him, and we know it's coming."

[RELATED: How Shanahan's lack of aggressiveness cost 49ers before]

Juszczyk, a Harvard alumnus, is a smart guy. The negativity has already begun to flow, and it's going to be quite some time until the faucet is turned all the way off. It won't be coming from within the locker room, though, and that will be key as the 49ers try to get back to the Super Bowl next year.