The trip started with a runway mishap that dented the team’s charter plane, forcing a change of departure airports and delaying by six hours the arrival at their New Jersey hotel.

It continued on the second leg of their 10-day road trip with a truck containing an MRI machine breaking down before it arrived at the resort in West Virginia where the 49ers are staying between their Week 2 and 3 games.

If you ever wanted a metaphor for the early part of the 49ers' season it's this: The device used to diagnose injuries ends up on the inactive list.

Between those two bizarre occurrences, the really bad stuff happened to the 49ers.

The 49ers beat the New York Jets on Sunday. But the team -- or what was left of it -- departed MetLife Stadium beaten and deflated due to a number of significant injuries to key members of the team.

The injury list included quarterback Jimmy Garoppolo, running backs Raheem Mostert and Tevin Coleman, and defensive linemen Nick Bosa, Solomon Thomas and D.J. Jones.

Bosa and Thomas sustained ACL tears, the 49ers confirmed Monday. Both will undergo season-ending surgeries.

Bosa’s injury, above all the others, was a gut punch because of his importance to the present and future of the franchise. He emerged last season as a rookie into one of the NFL’s defensive stars and an irreplaceable presence in the 49ers' defense.

 

Injuries are a part of the game.

And no consideration is given in the standings to bad luck.

Coach Kyle Shanahan knows the upcoming opponents on the schedule are not spending any time feeling sorry about the 49ers’ lengthy injury report.

But before the 49ers moved on to their preparations to face the New York Giants, Shanahan allowed himself and his staff some time to get salty and vent amongst themselves.

“This was one that (we) felt really good about the win, but we had some time to b---h a little bit about some of our unluckiness with injuries, especially taking the plane ride together and being here last night at the hotel together,” Shanahan said.

The 49ers have a day or so to regroup and connect as a team at The Greenbrier Resort in White Sulphur Springs, W.Va. The team chose that location because of the short flights to and from New Jersey, where they return to MetLife Stadium to face the Giants on Sunday.

The club also selected The Greenbrier because of the availability of pristine natural grass practice fields – to minimize the strain each player will experience on his lower body. If the 49ers never see another artificial surface field, that will be all right with them.

The season is not lost for the 49ers, though there is less reason for optimism than when the season started. Coming off a bitter Super Bowl defeat, there was only one way the 49ers and their fan base were going to measure this season.

It was Super Bowl or bust.

And, now, the 49ers are busted.

They are just trying to keep things together until some of their top players – George Kittle, Deebo Samuel, Richard Sherman among them – get back on the field.

This feels a lot like the 2018 season. The 49ers entered that season with high expectations. But running back Jerick McKinnon, who was expected to be a focal point of the offense, sustained a season-ending knee injury a week before the opener. Three weeks later, Garoppolo was lost for the season with a knee injury of his own.

The 49ers fell apart.

Out of that mess came something good. The 49ers were 4-12, placing them in position to grab Bosa with the No. 2 overall draft pick.

This team is not heading toward the same crash-and-burn scenario of 2018. This team can still win a lot of games because the roster is in a much-better state than the mess former general manager Trent Baalke left behind.

After giving himself a night of high-volume four-letter-word usage, Shanahan sees this as a situation in which all is not lost.

“It’s also a good challenge, too,” he said. “We are a lot more equipped for this than we were a few years ago.

“When you lose some guys, we got a lot of other good guys, too. You can’t replace some of those guys we lost, of course. But, collectively, I know we got a good team and it’s not just me who feels that. I know our players know that. I know a lot of guys are excited for their opportunities.”