For the courageous fans who decided to spend their Sunday evenings being battered by a constant, record-setting downpour, and wind gusts pushing north of 20 miles per hour in Santa Clara, there will be some unpleasant memories about the 49ers’ 30-18 loss to the Indianapolis Colts.

As brutal as the conditions were — and they were brutal — there were early glimpses of optimism. It began in the form of an eight-play, 78-yard touchdown drive led by Elijah Mitchell’s five carries for 57 yards and a touchdown.

It was followed up immediately with a defensive jolt. Josh Norman punched out Jonathan Taylor’s first carry, and Fred Warner used his feet and some sort of magic to come up with the recovery.

But that recovery, deep in the Colts’ half, was only rewarded with a field goal. The Colts responded with an impressive touchdown drive of their own.

San Francisco’s own response was an career-long, 56-yard field goal with the wind, to put the 49ers up 12-7.

For the next 34-plus minutes, the 49ers offense went silent. The bootlegs Jimmy Garoppolo ran successfully on the first drive were nowhere to be found. For five-straight drives, stretching from the start of the second quarter through the start of the fourth quarter, the offense went three-and-out every single time.

Kyle Shanahan was so conservative and discernibly distrustful of his offense that, with the Colts on the 49ers’ one-yard line on third down and 1:50 left in the first half, he failed to call a timeout. After Carson Wentz scored a touchdown with about a minute left, Shanahan opted to burn the clock, while also knowing that Indianapolis would receive the ball in the second half.

It felt as if the 49ers were watching the game like a passenger. There were no signs of life, no reason to believe this team would step out of its stupor.

Everything they could not afford to do, they did. Four times they committed defensive pass interference penalties for massive chunks of yardage. Those penalties were legitimately the Colts’ best offense.

As they have for the past two games, the 49ers struggled severely on third down, going an embarrassing 1-for-11 in that respect.

And of course, there were the turnovers. Despite a gifted shovel pass interception from Wentz to Azeez Al-Shaair in the first half, the 49ers went three-and-out on that drive, and despite having a 2-0 turnover advantage at that point, they went on to lose that battle.

A Deebo Samuel fumble trying recklessly to get extra yardage, a Jimmy Garoppolo sack fumble after escaping pressure, a Garoppolo interception trying to target Samuel, then another Garoppolo interception after the game was out of reach, in the waning minutes. That interception was the least meaningful, but perhaps the most embarrassing, thrown into triple coverage, and nowhere near the 6’3″ Jauan Jennings.

This was not a loss caused by the rain. It was a loss caused by all the things which had plagued them over the past three games, defined, most of all by a failure to be disciplined, a lack of creativity, and an overall recklessness in multiple areas of the game.

In apropos fashion, this game ended with a sack of Jimmy Garoppolo by DeForest Buckner.

At 2-4, the 49ers appear nowhere near contending, and with no first-round pick, there’s no silver lining, especially with their rookie quarterback still on the mend, and the head coach indicating he’s not willing to start him when he returns. These are dark times for the 49ers indeed.