ESPN

Sometimes, Kevin Towers, the longtime general manager of the San Diego Padres, catches himself thinking about the most recent important game his team played and wondering: What if?

What if the Padres had been able to close out the Colorado Rockies in the National League wild-card play-in game at the end of the 2007 season? What if the Padres -- and not the streaking Rockies -- had moved on to meet the Philadelphia Phillies in the NL Division Series? What if the Padres had ridden the momentum of that 163rd game deep into the postseason, perhaps all the way to the World Series?

Would things somehow be different now?

All Towers knows is this: It's been all downhill for the franchise since then.

"That's when it all started," Towers said. "Nothing really good has happened since then. We might be in a completely different situation now than where we're at. There haven't been many bright spots since."

Towers is being diplomatic. Like a plummeting stock price, the Padres have been in free fall. The Padres lost 99 games this past season and finished last in arguably the worst division in baseball, the National League West. But it wasn't just about where the Padres finished, it also was about how they got there.

"I've had less-talented clubs than this," Towers said. "But everything went wrong. We just didn't perform well on the field. I don't think we had more than a week or 10 days where we played well. That [four-game] sweep of the Mets [in June] was probably the highlight of our season."

The Padres had to contend with injuries. Shortstop Khalil Greene punched out an equipment locker and broke his hand. Second baseman Tadahito Iguchi somehow separated his shoulder while trying to avoid being hit by a ball on the base paths. And pitcher Chris Young and catcher Josh Bard were injured by the same player in the same inning during a game in May. National League MVP Albert Pujols first hit a line drive off Young's face, breaking his nose. Later in the inning, Pujols collided with Bard at the plate, spraining the catcher's ankle.

It was that kind of season.

If the Padres had won that play-in game with the Rockies -- and remember, they took the lead after scoring two runs in the top of the 13th, only to have the Rockies rally for three of their own in the bottom of the inning -- they would have made three straight playoff appearances, the best stretch in franchise history.

They narrowly avoided a 100-loss season, can't afford to re-sign the second-most popular player in franchise history (Trevor Hoffman) and have been forced into shopping staff ace Jake Peavy.

Is this all a bad dream?

"It's very, very frustrating," Towers conceded.

And thanks to matters beyond Towers' control, things could worsen before they improve. The Padres are bracing for a significant drop-off in attendance in 2009, thanks in equal parts to the economic downturn and their dismal performance this past season.

In 2007, the Padres drew 2.8 million visitors to Petco Park. Last year, that figure dipped to 2.4 million. It would surprise few if the Padres were to draw less than 2 million in attendance next season.

Then there is the soap opera surrounding the team's ownership. Owner John Moores, one of baseball commissioner Bud Selig's closest allies, is in the throes of a nasty divorce from his wife, Becky, and custody of the franchise -- like with a child -- is at stake.

To cut costs, Moores has ordered a slashing of the payroll. Hoffman, baseball's all-time saves leader and the face of the franchise, was angered when the Padres pulled back their $4 million offer for next year. He expects to finish his career elsewhere. Towers has been openly soliciting offers for Peavy.

The payroll, which was $73 million for the 2008 season, is likely to be sliced nearly in half for the 2009 season, forcing Towers' hand.

"It's kind of difficult to have one player eat up a quarter of your payroll," Towers said. "We lost 99 games with Jake, and we're not going to get better by keeping him and his salary."

Although talks with Atlanta and the Cubs have been on-again, off-again, the hope is that Towers can land three or four low-cost, high-ceiling players and begin the team's rebuilding. There's precedent: Before the 2006 season, he swapped pitchers Adam Eaton and Akinori Otsuka to Texas and got Young and first baseman Adrian Gonzalez in return.

But beyond the payroll limits in place, there are constraints as Towers goes about the task of reshaping the Padres. Special assistant Paul DePodesta, the former Los Angeles Dodgers GM, reports not to Towers but directly to CEO Sandy Alderson and must sign off on player moves.

"It's a mess," an industry executive said about the situation. "That whole organization is totally dysfunctional."

It hasn't helped that the Padres haven't drafted well. Matt Bush, the No. 1 overall pick in the 2004 draft, was a bust at shortstop before being converted to pitcher, then underwent Tommy John surgery. Pitching prospect Cesar Carrillo, San Diego's top pick and the No. 18 overall selection in 2005, also has been derailed by arm problems.

There is some hope that outfielders Chase Headley and Will Venable, as well as other young players, will continue to develop and move the Padres in the direction of respectability.

It helps that the NL West, the division that the Padres had seemed on the verge of dominating just a few short years ago, is home to a few other teams that must share the Padres' blueprint and develop from within, which is to say, at modest cost.

"Other than the Dodgers, it's a winnable division," Towers said. "It really boils down to our young players. For us to have consistent success, we need them to come through."

The rest, Towers understands, is out of his control.

"It's a daunting task that lies in front of us," he said. "But we welcome the challenge. Hopefully, we'll make some good baseball trades and get back to where we want to be. Is it a tough sell? Definitely. But compared to 1993 and 1994, when we had that fire sale, we're in a much better position."

But the Padres are a long, long way from that night 13 months ago at Coors Field when they were three outs away from their third straight playoff spot.

Sean McAdam of the Boston Herald covers baseball for ESPN.com.