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Once NFL commissioner Roger Goodell flexed his Article 46 muscles and threatened to suspend the players implicated in the Al Jazeera PED report if they didn’t cooperate with his investigation, those players had little choice but cooperate.

But for Packers linebacker Clay Matthews — who was cleared alongside teammate Julius Peppers and Steelers linebacker James Harrison because of a lack of credible evidence — being cleared still comes with a cost, one that he’s “obviously not happy” about.

Via Ryan Wood of the Green Bay Press-Gazette, Matthews said he was troubled by the fact it became a league-union power struggle, one which his side lost in a rout.

“That’s why we stuck strong with the PA in regards to this,” Matthews said. “Just because it sets a dangerous precedent. I think this is something that’ll come up within the next negotiations, CBA negotiations. It’s a very dangerous precedent.”

At the same time, Matthews said they weren’t prepared to be martyrs to the cause at the cost of being suspended from their teams.

“We weren’t ready to fall on the knife for something we’ve maintained our innocence about,” Matthews said. “Obviously, the interview proved that [we were innocent]. It’s exactly that. Especially with the regular season starting, yeah, it’s good to get all that behind us and focused on the regular season starting with Jacksonville next week.”

Peppers described months of “back and forth” with the NFLPA on the best way to handle it, and said his interview with the league took about an hour. And like Matthews, the veteran pass-rusher said he was disappointed that allegations which were recanted in a report by a network that no longer exists became an issue that took up an offseason.

“It was a slow time during the NFL, I guess,” Peppers said. “It got a little bit more attention than it deserved, in my opinion. It’s unfortunate that we as NFL players are always open to innuendo and rumors and stuff. That’s something that’s unfortunate that players are going to have to deal with.”

Their only chance to deal with it now will come at the collective bargaining table, as the topic of Goodell’s control over player punishment figures to become one of the primary sticking points in future negotiations. But as Matthews and Peppers and Harrison found out when they had to toe the line, that power isn’t something the league is likely to give up lightly.