New Orleans — There were 100 million reasons for Saints fans to smile last week. Drew Brees signed the richest per-season contract in NFL history.

It was a rare moment in New Orleans. There hasn’t been much joy there since a playoff loss to San Francisco in January.

Even getting the Brees deal done hardly camouflages the other problems that have plagued the franchise this year — woes that easily could linger through the upcoming season. Brees knows it. So does exiled head coach Sean Payton and linebacker Jonathan Vilma, both suspended for the 2012 season for their roles in the bounty program an NFL investigation unveiled.

Also gone for the first six games of the schedule will be Joe Vitt, who has taken over for Payton as head man to guide the team through training camp and preseason games. Who will replace Vitt when he begins his suspension remains uncertain, but continuity will take another hit in the Big Easy.

The Saints also will be without primary pass rusher Will Smith; the defensive end got a four-game docking.

Other than Brees’ return for five years and $100 million, there’s barely been a positive blip on the New Orleans radar all year.

“It’s been a little surreal just because of the process throughout the offseason, and just how challenging an offseason it’s been for everyone, obviously everyone within the Saints organization, this city,” Brees said. “It’s just been a crazy offseason and I think we’re all just ready to get back to work and excited that it’s all starting here in a week. It’s hard to believe.”

What is most difficult to believe is that the Saints won’t struggle at some juncture — or many junctures — with the challenges of what Tony Dungy calls “unknown territory.” “Everything is just different. It’s not like there is a book on this on how another team handled it,” said Dungy, who coached the Indianapolis Colts to the 2006 championship.

“What tends to happen in great organizations is you have stability and certain ways of doing things. Players know how to do things, and fortunately they will not change all that much for a veteran team. But they will change.

“How will the new coach run things as compared to how Sean ran them or how Joe Vitt is running them? There are little differences the players have to adjust to. Some things won’t manifest themselves until difficulties show up.”

Other, uh, difficulties include allegations of wire-tapping of the visiting coaches’ box during games in the Superdome.

Last month, the Saints hired a firm run by former FBI director Louis Freeh to conduct an internal investigation. Freeh, who oversaw the investigation of Penn State’s actions in the Jerry Sandusky case, will look into anonymous claims that general manager Mickey Loomis had the ability to eavesdrop on opposing coaches’ radio communications during games between 2002 and 2004. The Saints have labeled the allegations “ludicrous” and “1,000 percent false.”

The Freeh Group will also investigate the bounties case.

One of the toughest hurdles will be keeping the NFL’s biggest offseason scandal from defining the Saints’ performances. With all the legal maneuverings, including Vilma’s defamation lawsuit against Commissioner Roger Goodell, likely to be drawn out, there’s no way the team can concentrate solely on football.

And you thought there already were enough distractions in New Orleans.

A defense that ranked 24th overall and 30th against the pass is missing two key playmakers, although signing Curtis Lofton as a free agent to step in for Vilma could solve some problems. The Saints also got little help in the draft, in part because they forfeited their second-round choice in the bounty scandal.

There’s also the significant question of how opponents will regard the Saints. Will there be any revenge factor for teams that feel their players were targeted in the past? Plus, the Saints could find themselves wondering whether on-field officials are looking extra closely at their hits — and reaching more quickly for their flags.

Dungy remembers joining the Steelers as a rookie in 1977, a year in which coach Chuck Noll was traveling to California to testify in a lawsuit brought against him by Raiders safety George Atkinson. The Steel Curtain was quite penetrable that season and didn’t make the playoffs.

“With that and the other distractions you can get, even if you have all your players back — and the Saints don’t — you are challenged,” he said.

Dungy also believes the NFC South will be improved, increasing the hazards for the Saints.

But they do have one asset no one else can claim: Brees.

“Having him will make a huge difference,” Dungy said. “They have got a lot of veteran players and they have the one definitive leader you need. He understands what it takes to win and they will rally around him. He is their one ace in the hole.”