EAST RUTHERFORD, N.J. — The Jets’ season has deteriorated into a tragicomic mix of fluky injuries and M.R.I. tubes, of turnovers and incompletions, of hoping for the best but assuming the worst.


For the second consecutive Sunday, there was an intense competition for the most worrisome aspect of their afternoon, and the contenders all looked the same: an inaccurate quarterback, an impotent running game, a porous defense and the image of a key player collapsing to the ground and being carted away, his status uncertain but grim — not unlike his team’s.


And yet somehow, the nadir of the Jets’ 34-0 loss to the San Francisco 49ers at MetLife Stadium came long after the outcome had been decided, after Santonio Holmes’s left leg gave out on a seemingly innocuous fourth-quarter catch along the sideline.


As Coach Rex Ryan stewed across the field, his anger and humiliation was building for the postgame tirade he would soon unleash at his players and at his news conference. All around him was red, the color of jersey-wearing 49ers fans who had moved down to claim seats belonging to Jets supporters who had opted to sit in traffic rather than watch the end of the game.


The totality of the carnage — the 2-for-13 ineptitude on third down; the 245 rushing yards allowed, the most under Ryan; the 145 yards amassed — infuriated Ryan, and he arrived in the interview room afterward looking like a man who needed a hug, a stiff drink or both. He started to say something, paused for six seconds, then apologized for the coarse language he was about to use.


“I was going to say we got our butt kicked,” said Ryan, who thought better (or worse) of it and opted for more colorful terms to characterize the nature of the defeat.


Just minutes earlier, Ryan told his players that San Francisco embarrassed them, that their performance was “obviously unacceptable.” He told them not to bother coming to the facility Monday or Tuesday, that they would be best served spending that time reflecting on their own. Summing up the day, Joe McKnight said, “I ain’t never seen anything like that.”


The A.F.C. East standings indicate that the Jets are still in first place, sharing the same 2-2 record as the New England Patriots and the Buffalo Bills. But with undefeated Houston — a team that is capable of bullying the Jets just as the 49ers did — visiting next Monday night, the Jets’ stay in first could soon end.


Not without their best player, Darrelle Revis, who sustained a season-ending knee injury last week, or their best offensive player, Holmes, who seemed in such deep pain that, while lying on his back, he could not bear holding onto the ball. He flipped it in the air, and Carlos Rogers returned it 51 yards for a touchdown.


And not when a coach is asked about the job security of a quarterback, Mark Sanchez, who committed two of the team’s four turnovers, who has presided over an offense that has scored a single touchdown in its last 34 possessions, who through four games has completed 49.2 percent of his passes. And not when a coach is seething about a defense that has allowed an average of 172.8 rushing yards and is better at missing tackles than making them.


“They ran the football, they controlled the clock, and we didn’t do anything to stop them,” linebacker Aaron Maybin said. “As a defense, that’s pretty embarrassing.”


Several times Ryan had proclaimed this team the best of his four-year tenure, but one quarter into the season, the Jets are ravaged by injuries, inconsistency and, perhaps, miscalculations.


The defense they thought would be excellent is not, yielding 379 yards Sunday. The running game they thought would thrive under the new coordinator has sputtered, recording only 45 yards. With their passing offense already diminished by the absences of the receiving threats Dustin Keller (hamstring) and Stephen Hill (hamstring), the Jets’ lack of depth was further exposed by Holmes’s injury. They strengthened other areas of need in the off-season, like safety, but opted not to acquire a proven No. 2 receiver to complement Holmes. Now they are facing the consequences. Holmes left the stadium on a golf cart, with crutches, his foot encased in a boot. X-rays were negative, but Holmes will have a magnetic resonance imaging test Monday.


“What are we going to do?” Sanchez said. “We can’t just not show up. We’ve got to play. We’ve got to play better than we did today.”


Sanchez completed 13 of 29 passes for 103 yards, committing two turnovers — one, a fumble after he held the ball too long, was particularly vexing, stalling a drive at the San Francisco 25 late in the first half with the Jets trailing, 7-0. The 49ers countered with a field goal as time expired, and early in the third quarter, after a Sanchez screen pass was deflected and intercepted, a brief but audible chant arose.


It took four games — and the second at home — for some fans to call for Tebow. It was unclear precisely why, given his minimal role Sunday (2 rushes for no yards and a pass for 9 yards). In the first half alone, the 49ers revealed more creativity with their change-of-pace quarterback, Colin Kaepernick — who ran for 50 yards and the team’s first touchdown — than the Jets have all season with Tebow.


Several players defended Sanchez afterward, as did Ryan, who said he was not ready to switch quarterbacks because “I think Mark is the answer.”


But, he added, “Again, time will tell.”


And there is time. Twelve more games for Sanchez to rebound, for the defense to recover, for players to heal. But with 12 more games also comes the potential for 12 more exasperating losses, 12 ways the season could spiral out of control. As always, the Jets are hoping for the best. Hoping, perhaps, against hope.