Jim Leonhard (36) disrupts a pass intended for the Browns' Benjamin Watson in Cleveland on Nov. 14. Getty Images

FLORHAM PARK, N.J.—Jim Leonhard's teammates leaned on him for leadership and advice. Cornerback Drew Coleman recalled a tip that Mr. Leonhard gave him about wide receivers: Watch their hands as they approach the line of scrimmage, and expect a pass play if they tighten their gloves.

It was one of the countless intangibles that Mr. Leonhard, the Jets' 5-foot-8, 188-pound safety, brought to the field and the locker room, and he was lost for the season when he broke his right shin last Friday. His teammates are feeling his absence, which was painfully apparent when they absorbed a 45-3 pounding at the hands of the New England Patriots on Monday night.

Mr. Leonhard was one of the defense's signal callers, and the Jets (9-3, 3-1 in the AFC East) have been working at practice this week to regroup in time for Sunday's game against the Miami Dolphins (6-6, 1-2) at New Meadowlands Stadium.

When Mr. Leonhard collided with wide receiver Patrick Turner at practice last week, his teammates expected him to pop back up. After all, this was the same guy who stayed in a game against the Jacksonville Jaguars last season after he shattered his thumb making a tackle. He underwent surgery the following morning, then played six days later against the Patriots with three metal pins in his hand.

"It didn't feel good, that's for sure," he said in an interview earlier this season.

In other words, it takes an almost catastrophic injury for Mr. Leonhard to miss time. So his teammates knew something was wrong last week when a cart arrived to wheel him away from the practice field. The episode had a psychic impact on the team.

"I think we were all crushed," defensive coordinator Mike Pettine said. "It's just—it was really stunning."

On Saturday, Mr. Leonhard underwent season-ending surgery. On Sunday, defensive tackle Sione Pouha visited him at the hospital. On Monday, the Jets got demolished by the Patriots. It was the team's most trying 72 hours of the season.

Leonhard and Jets coach Rex Ryan confer during Oct. 17 game in Denver. Associated Press

"I think everyone just has to do a little bit more to fill that void," Mr. Pouha said. "Every man has to be accountable for his own position."

In a lot of ways, Mr. Leonhard personified the Jets' chip-on-the-shoulder ethos. An undrafted free agent out of the University of Wisconsin, he was considered too small for the NFL. So he came up through the league the hard way, earning his reps, silencing his skeptics.

Signed by the Jets before the start of last season, he quickly emerged as one of the defense's more indispensable players. He was not a big talker, and in that sense he was an atypical presence in a locker room that took its cue from outspoken coach Rex Ryan. But Mr. Leonhard radiated confidence during games, and his teammates—many of them a half-foot taller, many of them at least 50 pounds heavier—turned to him for guidance.

"Once he gets on the field, he's like a totally different person," Mr. Coleman said. "He had so much swag. And he didn't just know his job; he knew everybody's job. He was like a coach for the defense. If anybody slips up, he's on top of it."

Mr. Coleman curiously shifted between the past and present tenses in describing Mr. Leonhard, and there was symbolism in this: As much as his teammates still recognize Mr. Leonhard as part of the team, he can no longer help them this season. What he did is done, a victim of a violent sport.

From a statistical standpoint, Mr. Leonhard was on pace for a career year in his sixth NFL season. He already had a career-best 57 tackles, four passes defended, a fumble recovery and an interception. He also averaged 11.3 yards per punt return, which ranked among the league's best.

Even more important, Mr. Leonhard had vital responsibilities as the secondary's signal caller. He was the player who communicated reads to the other defensive backs who were on the field. Mr. Pouha likened Mr. Leonhard to a radio antennae. "He's the one who brings the frequencies in, gets the calls out," Mr. Pouha said.

Mr. Leonhard did this while working in concert with David Harris, who, from his linebacker position, serves as the nerve center for the defensive line, repositioning the tackles and ends depending on the play call.

To the untrained eye, the Jets' defense can seem simple. Cornerbacks Darrelle Revis and Antonio Cromartie play man-to-man coverage, but what happens when a tight end lines up wide? Or when the Jets bring an extra man (or two) to the line for a blitz? Or when the team is in a nickel package, with five defensive backs? Or in a dime, with six? It was Mr. Leonhard's job to make certain his teammates were on the same page.

"If he's down on the line, he might say something like, 'This is a tough cover for you. I'll get this cover and you blitz,'" linebacker Jamaal Westerman said. "Being in this defense for so long, he knows where all the parts are supposed to fit. And how they best fit."

Mr. Leonhard used verbal cues and hand signals to relay this information, and this is standard across the league. Every defense has a Mr. Leonhard, though some are more effective communicators than others. "He really did quarterback the back end," Mr. Pettine said of Mr. Leonhard's role.

Bill Romanowski, a former linebacker who spent 16 seasons in the NFL, said he had a similar role. When he was with the San Francisco 49ers at the start of his career, he was constantly exchanging information with safety Ronnie Lott, who was responsible for the secondary. Later, with the Denver Broncos, Mr. Romanowski said his duties expanded and he became the point man when it came to recognizing offensive schemes. Mr. Romanowski said he often had to make split-second decisions based on what he saw before the snap.

If he wanted the secondary to be in "Cover 1," which is man-to-man coverage for all the defensive backs but one, Mr. Romanowski would touch the top of his helmet. If he wanted the defense to be in "Cover 2," he would touch his shoulders. And so forth. On any given snap, he also would determine whether to dispatch a defensive back or a linebacker as a "robber"—someone to provide double coverage on a receiver downfield.

"These schemes are really, really complex," said Mr. Romanowski, who estimated he had to know between 75 and 100 defensive variations each game. "And when you lose a guy like Jim, there's no question that's a huge blow to them. He's the glue out there, and I think it hurts."

At the same time, Mr. Romanowski said the Jets, even with Mr. Leonhard, likely would have had a hard time slowing Patriots quarterback Tom Brady, who eviscerated them by completing 21 of 29 passes for 326 yards. But there was little question that Mr. Brady preyed on a defense that was disorganized. On one pass play, defensive tackle Mike Devito somehow found himself matched up against scatback Danny Woodhead. It led to a 35-yard gain.

Mr. Coleman said teams often try to bunch receivers together before the snap to create confusion and miscommunication, and that appeared to be Mr. Brady's modus operandi at times.

In Mr. Leonhard's absence, Mr. Ryan is hoping for more of a collective effort. Safety Brodney Pool said practices this week have been solid, with the secondary working to recover from Mr. Leonhard's abrupt exit. The coaches also want safety Eric Smith to take on more of a vocal role as Mr. Leonhard's surrogate, though that tends to go against his nature.

"I don't really say much," Mr. Smith said. "What needs to be said, that's what I say. So when it comes to communicating on the field, that's no problem. It's something I've been used to doing ever since college, making calls."

There is scant margin for error. Safety James Ihedigbo, who also was expected to play more, sprained his ankle against the Patriots and is doubtful for Sunday's game. The Jets have called on some unheralded reinforcements, including safety Emanuel Cook, who was most recently with the Hartford Colonials of the United Football League, the equivalent of football's farm system.

As for Mr. Leonhard, he went home after surgery—doctors inserted a rod in his leg—to convalesce and begin his rehab. On Thursday, he returned to the practice facility for the first time, negotiating the hallways on a scooter. His practice jersey remained in his locker.

Write to Scott Cacciola at scott.cacciola@wsj.com