The NFL Commissioner re-issued penalties Tuesday for the four players disciplined in the New Orleans Saints bounty scandal, and after a series of appeals, questions about the league's evidence and a pending defamation suit brought forward by Jonathan Vilma, the punishment stemming from the pay-to-injure program has been tweaked.

For now.

Vilma, the New Orleans Saints linebacker who would have been eligible to return from the physically-unable-to-perform list this week, is still essentially suspended for the season.

But he gets to keep the six game checks due for his time on the PUP list.

Scott Fujita, now a Cleveland Browns linebacker, is suspended for one game after originally being docked for three games.

Anthony Hargrove, a defensive tackle without a team, had his suspension reduced by a game to seven gamers, but receives credit for time served during the five weeks he has been a free agent. If he is re-signed by a team, he must miss two games.

The four-game suspension for Saints defensive end Will Smith is unchanged.

Goodell was ordered to reconsider the punishment after a three-member panel of judges, hearing an appeal by the NFL Players Association (NFLPA), temporarily lifted the suspensions on Sept. 7, but affirmed the Commissioner's authority to discipline players for "conduct detrimental to the game."

Before reaching his decision, Goodell met with each of the disciplined players within the past two weeks. Such meetings never occurred before the original punishment was announced in May, with the league contending that the players refused to cooperate and the players charging that the league's investigation and process was faulty.

"The quality, specificity and scope of the evidence supporting the findings of conduct detrimental are far greater and more extensive than ordinarily available in such cases," Goodell wrote in a memo the NFL clubs.

"In my recent meetings with the players and their counsel, the players addressed the allegations and had an opportunity to tell their side of the story. In those meetings, the players confirmed many of the key facts disclosed in our investigation, most particularly that the program offered cash rewards for 'cart-offs,' that players were encouraged to 'crank up the John Deere tractor' and have their opponents carted off the field, and that rewards were offered and paid for plays that resulted in opposing players having to leave the field of play."

What now?

The players can appeal the discipline again to Goodell or pursue more court action, including a federal case that the NFLPA filed on behalf of the three players separate from Vilma. And it's still unclear whether Vilma will revise the legal strategy that resulted in his defamation case against Goodell.

Vilma's attorney, Peter Ginsberg, did not immediately return calls from USA TODAY Sports.

The NFLPA indicated that it hardly sees the issue as closed.

"For more than six months, the NFL has ignored the facts, abused the process outlined in our collective bargaining agreement and failed to produce evidence that the players intended to injure anyone, ever," the NFLPA said in a statement. "The only evidence that exists is the League's gross violation of fair due process, transparency and impartiality during this process. Truth and fairness have been the casualties of the league's refusal to admit that it might have made a mistake.

"We will review this decision thoroughly and review all options to protect our players' rights with vigilance."

The league initially suspended Vilma, Fujita, Hargrove and Smith on May 2, citing "conduct detrimental to the NFL" and "their leadership roles in the New Orleans Saints' pay-for-performance/bounty program that endangered player safety over three seasons from 2009-2011."

A dizzying array of appeals, grievances, court filings, lawsuits and arbitration hearings ensued with the most recent one ultimately allowing the players to return to the field after a three-member panel consisting of of retired federal Judge Fern Smith, retired federal Judge Richard Howell, and Georgetown professor James Oldham lifted the suspensions Sept. 7, ruling the Goodell had overstepped his authority by lumping the illegal incentives of the Saints' program into his decision.

Vilma has not played this season and currently resides on the Saints' physically unable to perform list as he recovers from a left knee injury.

Smith, who didn't miss a game since the appeal was lifted, has 22 tackles and two sacks for the Saints.

Fujita missed the Cleveland Browns' first game with an injury but has compiled 14 tackles and one sack in four games since.

Hargrove signed with the Green Bay Packers in March but was released in training camp and has not latched on with a new team.

Prior to the issuance of the player punishments, Goodell suspended Saints head coach Sean Payton for the entire 2012 season, banned former defensive coordinator Gregg Williams (who had assumed a similar role with the St. Louis Rams) indefinitely while giving lesser punishments to Saints General Manager Mickey Loomis (8 games) and assistant head coach Joe Vitt (6 games) on March 21.

Jarrett Bell, USA TODAY Sports