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IRVING, Texas – The Cowboys’ biggest fears have become a reality regarding one of their most productive players.

Sean Lee’s season is over.

The inside linebacker who leads the team in tackles will need surgery to repair torn ligaments on his right big toe. The surgery is set for early next week but it’s likely Lee will be heading to injured reserve immediately.

Lee’s surgery will be similar to what running back Felix Jones had during his rookie season in 2008. Jones had a full recovery for the following season and the Cowboys are expecting the same for Lee in 2013.

With the NFC East leading Giants (5-2) coming to town Sunday at Cowboys Stadium, followed by the Cowboys traveling to Atlanta to face the undefeated Falcons the next week, it’s a bad time for the defense to be without one of their top two players.

The Cowboys have not officially made an announcement on Lee but it’s likely coach Jason Garrett will address the situation at his regular press conference at 10:05 a.m. (CDT) at Valley Ranch Wednesday.

With Tuesday being the Cowboys’ day off, the team did not have any press conferences or an open locker room period. With Jerry Jones’ mother passing Tuesday morning, the Cowboys’ owner did not have his regular radio show as well. So there has been no official word from the Cowboys regarding Lee or any other injuries this week.

The team is expected to officially sign veteran safety Charlie Peprah on Wednesday. The Cowboys would have to clear a roster spot, but it’s not likely it would be an easy Peprah for Lee, who will go to IR. The Cowboys would need more depth at linebacker and might have to sign a veteran.

The Cowboys still have two punters - both Chris Jones and Brian Moorman – on the 53-man roster. Also, safety Matt Johnson is injured again and there have been discussions that he could land on IR, although head coach Jason Garrett said Monday he doesn’t think the Cowboys are ready to make such a move.

With Lee out, the Cowboys will turn to backup Dan Connor, a free agent pickup this offseason after spending four years with the Panthers. Connor has played a limited role on defense this year, but filled in for Lee in Carolina against his former team.

Connor, a college teammate of Lee at Penn State, has 14 tackles this year but will likely take over as the starter next to Bruce Carter.

Lee suffered the injury in the second half in Carolina on Sunday. He tried to fight through the pain but eventually took himself out, later saying he was simply “hurting the team by being out there.”

Through six games, Lee leads the Cowboys with 77 tackles, considerably more than DeMarcus Ware, who is second on the team with 43 stops. Lee also has eight quarterback pressures, third behind only Anthony Spencer (12) and Ware (10).

Lee was on pace to record more than 204 tackles this season, averaging 12.8 per game. He already tied the Cowboys’ single-game record with 21 stops in the Seattle game back in Week 2.

Missing Lee for any time will be huge, but especially against the Giants. Last year, Lee had a clutch interception against Eli Manning in the game at Cowboys Stadium. This season, he forced a fumble in the season opener that took away a scoring opportunity for the Giants in the Cowboys’ 24-17 win over the defending champs.