By remaining on the roster through the second day of the NFL's waiver period Tuesday, the talented but troublesome wide receiver will get $15.25 million in guaranteed money over the next two seasons. A clause in Holmes' five-year, $45 million contract, signed last offseason, kicked in Wednesday morning.
Holmes' future appeared murky with the Jets after a tumultuous season in which he feuded with quarterback Mark Sanchez and the offensive line, and was benched during the season finale in Miami for arguing in the huddle.
Still, owner Woody Johnson, general manager Mike Tannenbaum and coach Rex Ryan all insisted that Holmes would remain with the team despite the squabbles.
Holmes, already guaranteed his salary for next season, had a $7.5 million guarantee for the 2013 season kick in after Tuesday. While the Jets could still theoretically cut him or try to trade him, the financial commitment makes that an unlikely scenario.
So, New York is stuck hoping that Holmes can work out his issues with his teammates — primarily Sanchez — and return to the playmaking form that Ryan and the Jets became so enamored of when they re-signed him last July.
"To dismiss some of the good things that Santonio has done for the two years he's been here, he's been a tremendous player for us," Ryan said on Jan. 2. "He's won a ton of games for this franchise. And he's been a good teammate."
Johnson said a few weeks ago that the team intended to bring Holmes back, and it had nothing to do with his big contract.
"He may be one of the best players we've ever had here," Johnson said. "I think you could look at his talent level as extraordinarily talented."
Holmes, acquired from Pittsburgh in 2010 for a fifth-round draft pick, played a key role in the Jets' run to their second straight AFC championship game two seasons ago. But things turned sour for the former Super Bowl MVP this past season.
He openly criticized the Jets' offensive line for not giving Sanchez enough time to throw downfield, and ESPNNewYork.com reported that the two clashed at a late-season meeting. Several players questioned Holmes' captaincy throughout the season.
The capper came during the Jets' loss to the Dolphins, when former offensive coordinator Brian Schottenheimer benched Holmes after he argued with teammates in the huddle. The television broadcast caught Holmes being restrained by tight end Dustin Keller on the field as the wide receiver and right tackle Wayne Hunter yelled at each other. Holmes sat on the bench sulking late in the game while the Jets came up short in a bid to beat the Dolphins.
He finished with 51 receptions for a career-low 654 yards, while also catching eight touchdown passes.
Ryan acknowledged he made a mistake by not having "the pulse" of the locker room and for naming the team's six captains, including Holmes. He said no one will wear the captain's "C'' on their jersey anymore, adding that it's imperative the take a larger role on the offense and instill the team chemistry that was clearly lacking as the Jets finished 8-8 and missed the playoffs.
"There's a lot of positive things about Santonio," Ryan said. "Are there some things that we need to get corrected? Absolutely. And it's not just with him, but others as well."
Ryan told reporters last week at the Super Bowl in Indianapolis that Sanchez and Holmes spoke by phone and were planning to get together soon to try to work things out. Neither player has spoken to the media since the season ended, although Holmes sent a message on Twitter the day before the Super Bowl to Sanchez and nose tackle Sione Pouha saying: "Hope your getting as antsy as me for the 2012-13 season to start. One more day til we start to make that journey."