SANTA CLARA Drew Brees was desperate.
In January 2004, the then-Chargers quarterback was coming off a season in which he had gone 2-9 as the starter. He'd thrown 15 interceptions and 11 touchdown passes, was benched for five games and finished with a 67.5 passer rating, the 28th-best that season.
When Chargers officials met with Brees after the season, they were blunt: They told him they either were going to draft his replacement or find one in free agency. To Brees, the thought of losing the job he had fought so hard to attain was unacceptable.
"Nothing was given to me; (I) earned it. Then all of a sudden I was in a position where all of this was about to be taken away from me," he recalled in a recent phone interview. "And I'd say I was in a vulnerable spot. I had always been an extremely confident person. And yet things just weren't happening for me."
That frustration drove Brees to a former left-handed relief pitcher who spent eight years in the major leagues in the 1970s. Tom House was up front with Brees about knowing nothing about Cover 2 defenses or seven-step drops.
What he did know was how to break down a big-league pitcher from what he ate to how he slept to the most minuscule motions of hurling a ball and House agreed to focus his analytical arsenal on the struggling quarterback.
Today Brees talks about that initial session with House as if it were a life raft, the platform he used to regain his focus and retake control of his career. He said he speaks to House at least once a week during the football season.
So when Alex Smith, a fellow quarterback he had admired from afar, asked about House at the Super Bowl in February, Brees didn't hesitate to make an introduction.
"He (Smith) said he had some things mechanically he had to work on the shoulder and that kind of thing," Brees said. "And I said, 'There's no better guy to do that than Tom House.' "
The NFL is a multibillion-dollar industry, and quarterbacks are its most cherished asset. They marry supermodels and date pop stars. Rules have been changed to protect them from injury. On rosters of 53 players, they can account for 20 percent of the team's payroll.
But Smith said "only a couple" of coaches over his career have concentrated on mechanics. Whether it's because coaches simply don't have time to dissect individual throwing motions or there's a fear of making passers robotic in a sport in which adaption is key, quarterbacks simply don't get the kind of arm attention pitchers do.
"It's big business in baseball," Smith said. "But there's nobody in football."
House, 65, works with about 1,100 pitchers a year at the Rod Dedeaux Research and Baseball Institute at USC, including clinics with Little Leaguers and sessions with professional players. Giants pitcher Barry Zito, for example, worked with House this past winter.
A different kind of thrower, however, recently has come to House seeking the same edge Brees received in 2004.
Baltimore's Joe Flacco is a former pupil, while USC's Matt Barkley, a likely top-10 pick in the next draft, had an off-campus session. When Smith worked with House in March, he was joined by Oakland's Carson Palmer, New England's Tom Brady and Kansas City's Matt Cassel.
Smith's biggest issue was his throwing shoulder.
In 2007, 301-pound Seahawks defender Rocky Bernard barreled through the 49ers' offensive line, slammed into Smith and drove the quarterback into the ground. Smith's right shoulder bore his own weight, Bernard's weight and the momentum from the charging defensive tackle. It separated, a process that tears the ligaments holding the joint in place. Smith needed surgery to repair it.
He was recovering the following year when he attempted a deep pass in practice. The motion tore a suture that had been inserted during the previous procedure, which dislodged a chunk of bone from his shoulder. He was placed on injured reserve, and his 2008 season was done.
At USC in March, Smith and the others looked as if they were filming a scene in "Avatar." They wore light-sensitive dots on their joints and stepped in front of 10 cameras, which took up to 1,000 frames a second as the quarterbacks went through their throwing motions.
"It provides you with data that your eyes can't see," House said of the three-dimensional analysis.
Through those images, House determined the 49ers quarterback still was affected by the injury suffered five years earlier. Following his surgeries, Smith had begun using his head as a lever shifting it slightly to the left to compensate for the lack of strength in his right shoulder.
And that threw his mechanics off balance.
"He knew where the ball had to be to get to an efficient release point, and he was changing body position to get to that release point inefficiently," House said.
House tweaked Smith's motion and also sent him back to Santa Clara with exercises designed to strengthen the shoulder, especially often ignored muscles in the back of the joint. Smith spent the 49ers' spring practices applying what he had learned.
"I think his mechanics have definitely improved," offensive coordinator Greg Roman said. "He works hard on them every day, and there's no question there's a real awareness. We tape the individual drills, and he'll watch those in really, really slo-mo. He's got a good feel for it right now."
For Brees, the issue was above his shoulder. House's analysis also includes a psychological test what House calls an "insight instrument" consisting of 300 word-association questions. He concluded that Brees was trying to please too many people and trying to do too much, a common denominator among the young quarterbacks he sees.
"As a quarterback, you think you can control everything," Brees said. "You feel like you should. And it's OK for you to have that mentality. That's why you're in that position. But in the end, there's only so much you can do. For me, in that '04 offseason, I was so angry and disappointed in the way the season had gone, that they were going to draft a guy. That was causing me stress."
The Chargers followed through on their warning to Brees by acquiring Philip Rivers, the fourth overall pick in the 2004 draft.
But a more relaxed and in-control Brees didn't relinquish his starting spot when the season began. Instead, he threw 27 touchdown passes and seven interceptions for the 12-4 Chargers, and his passer rating grew nearly 40 points.
Brees made the first of six Pro Bowls that season. In 2011, as a member of the Saints, he broke Dan Marino's 27-year-old record for most passing yards in a season.
New Orleans' season, of course, ended with a dramatic 36-32 playoff loss to Smith and the 49ers. But there's a brotherhood among quarterbacks, and Brees said he was eager to share his secret weapon House with Smith.
"It's been one tough break after another for him," Brees said. "And yet, you feel like he's always handled himself very well despite the circumstances and despite the tough situations. And so whenever you see a guy like that succeed like he was able to last year at our expense you still have to be very proud of the guy and happy for him."