49ers grades: For three quarters, it was San Francisco’s game to win.

OFFENSE

When your most effective runner is a wide receiver, that’s a problem. Deebo Samuel collected 53 yards on three carries, nearly equal to what Raheem Mostert (58) did on 12.

The 49ers finished with 141 rushing yards, but 66 of that came on three carries. Jimmy Garoppolo was solid early (9for-11 in the first half), but did have a forehead-slapping interception. In the second half, he was 11-for-20 for 130 yards.

With the Chiefs rallying past them, the 49ers’ last three possessions went: three-andout, seven-and-lost-on-downs, and two-and-an-interception.

DEFENSE

Out of gas or just a matter of time? In either case, the 49ers were able to keep the quickstrike ability of the Chiefs in check — until the fourth quarter.

Kansas City had three plays of at least 38 yards — and all came in the final quarter. Expand the lens a little wider and six of its 10 longest plays came in the fourth.

Richard Sherman and Jimmie Ward were in coverage on the two longest pass plays — which came in the final eight minutes.

Patrick Mahomes was sacked four times and threw two interceptions, but escaped enough times to rush for 29 yards, pass for 286 and be named MVP.

SPECIAL TEAMS

With the 49ers having fallen behind and needing a length-of-the-field drive to take the lead, Richie James opted to return the kickoff instead of letting it go into the end zone. He gained only 15 yards, part of a forgettable night on which he averaged 15.3 yards on four returns — he also muffed a punt in the first quarter, but recovered it. Robbie Gould made both of his field-goal tries (38 and 42 yards) to push his kicks-made streak to 17. He also converted two extra-point tries.

Mitch Wishnowsky averaged 43 yards on two punts — the first of which didn’t come until there were nine minutes left in the game.

COACHING

Fair or not, Kyle Shanahan now has two fourthquarter Super Bowl disintegrations attached to his name — one as the offensive coordinator in Atlanta three years ago and Sunday’s. He certainly wasn’t conservative out of the gate with Samuel’s skill-set on full display.

But Mostert — coming off a 220yard NFC title-game effort — didn’t run the ball until the nine-minute mark of the second quarter, Kyle Juszczyk appeared to have mismatches throughout but touched the ball only three times (all catches, for 39 yards and a TD) and Shanahan opted to not use timeouts near the end of the second quarter, settling for a halftime tie.

OVERALL

The 49ers were nine minutes away from winning the Super Bowl. Read that again: The team that went 12-36 in the previous three seasons (including 4-12 last season), had a chance to bring home the franchise’s sixth NFL title only to have it all slip away. The “if only” questions might linger for some time, but come next fall, the 49ers should be well positioned to continue their resurgence.