Roy Halladay signed a contract extension today that will guarantee him $60 million over three years, with a vesting option that would pay him another $20 million if he pitches enough innings in the first three years of the deal.

That’s the story here: Not the first trade, not the second trade, and not the third trade. The story here is that one of the best players in baseball took somewhere between 35-50 percent of his market value to facilitate a trade, leaving somewhere between $60 and $100 million in guaranteed money on the table. This is a staggering upset, one for which there is virtually no comparison in baseball history.

One year ago, CC Sabathia got $161 million in guaranteed money, an average of $23 million per season over seven seasons, as a full-fledged free agent. Two years ago, in a similar situation to that of Halladay, Johan Santana engineered a trade to the Mets and signed an extension totaling $137.5 million over six seasons, just shy of $23 million per season. Halladay, a bit older than both pitchers at the time of their deals but essentially even in value to both, took less guaranteed money per season across half the guaranteed years. To pull an example from this winter, John Lackey just got a guaranteed $82 million as a free agent. Halladay’s teammate for three years, A.J. Burnett, got a guaranteed $82 million one year ago. Neither Lackey nor Burnett has Halladay’s credentials. Lackey and Burnett have a combined 36 points in Cy Young voting in their careers; Halladay had 71 in just the 2008 vote alone, the third of four straight seasons in which he’s finished in the top five in AL Cy voting.

Halladay’s contract is so far removed from his market value that it looks like an error. Remember, he had to approve not only the contract, but the trade to the Phillies that precipitated it. He made the choice that he wanted to be with the Phillies so much-and wanted to be with them immediately so much-that it was worth it to him to leave $60 million, $80 million, maybe $100 million unclaimed. There is no way anyone could have predicted this even a few weeks ago. This is the kind of decision that a player gets to make for himself and his family. Halladay gets to play for a contender in 2010 and gets to do so with a team he wishes to play for, one that holds spring training near his Florida home, and he valued those things more than the marginal dollars foregone by not testing the market. I don’t judge him for it, but I do think we should all be stunned by how much money this man left on the table. There is no precedent for it in sports.

The extension Halladay signed justifies an otherwise unremarkable trade by the Phillies, who gave up three good prospects, including the heretofore untouchable Kyle Drabek, to bring in Halladay on the last season of his contract. That’s the kind of trade teams make all the time, dealing prospects for a player who can help them win when they’re at the peak of the success cycle, and for all the hype this trade has received, it’s not all that special in the abstract. The Phillies’ ability to get Halladay to sign a favorable extension, however, gives them an anchor in the years to come. It was worth sacrificing the prospects not for the 2010 season, but for the 2011-13, perhaps 2014, seasons to come, at the price they paid for those seasons.

Drabek is the prize of the deal, the son of Cy Young winner Doug Drabek and the Phillies’ first-round pick in 2006. After missing most of the 2008 season to Tommy John surgery, Drabek dominated the Florida State League and pitched well enough after a promotion to Double-A for the Phillies to refuse to deal him at the in-season trade deadline. His size-listed at 6’0″, 185 pounds-is a concern, especially for his anticipated role as a front-end starter, but his stuff and his performance have alleviated some of those concerns. Michael Taylor, prospect number two, followed up on his breakout 2008 with another strong year, making it to Triple-A in August and holding his own there. He’s become more disciplined as he’s come through the system, with better K/BB data at Triple-A than Double-A, and Double-A than High-A, without sacrificing the power that is his calling card. I like Domonic Brown’s speed and approach a bit better, but there’s nothing about Taylor that indicates he isn’t already close to the majors. As Kevin Goldstein noted last year, he gets high marks from the Phillies for his makeup as well. Travis D’Arnaud is a young catcher with a broad base of skills who spent the year in the Sally League. A supplemental first-round pick in 2007, D’Arnaud showed good power in 2009 for his league (52 extra-base hits, .164 ISO), with acceptable plate discipline and defense. His second half was much stronger than his first. He’s at least two years away, and has some development ahead of him to become an MLB catcher.

The Phillies, to some extent, paid in prospects instead of money for Halladay. The value he left on the table made it possible for the Phillies to trade perhaps their two best prospects and another top-ten guy to get him, because they’re not going to be so exposed on the back end of a monster extension.

This, in fact, gets to my biggest problem with the sequence: Roy Halladay just left $60 million on the table to come to Philadelphia. The Phillies couldn’t leave $9 million on it in pursuit of putting him on the best team in baseball? I appreciate Ruben Amaro Jr. consistently staying on point, labeling the Cliff Lee trade an exercise in refilling the farm system rather than in keeping the 2010 payroll below an arbitrary number. I do not, however, believe he is doing anything more than fronting for an absurd ownership initiative. The Phillies play in a taxpayer-funded ballpark, have been to back-to-back World Series-with all the direct revenue that generates-and will no doubt pack Citizens Bank Ballpark again in 2010 with another three million people paying even higher ticket, parking, concession, and souvenir prices. To trade away Cliff Lee in a blatant money move is utterly ridiculous under those circumstances, and worse still, turns the Roy Halladay trade into little more than a minor upgrade.

The gap between Halladay and Jamie Moyer, who has drifted to replacement level, is along the lines of six wins in a given season. The gap between Halladay and Lee might be one win. Or it might not. Going from Lee to Halladay is effectively a lateral move in the short term and takes nearly all the air out of the Halladay trade for the Phillies. They have essentially the same team today that they did yesterday, and given that the Blue Jays sent along six million bucks with Halladay, the same payroll that they did yesterday. They will be better for having Halladay the next three years, but at the moment, very little has changed for them other than that they don’t have as much depth to call on in 2010 should they need a starting pitcher or an outfielder. They took a prospect downgrade in the deal, getting back less than they dealt away, although that will be mitigated by having Halladay in the three or four seasons that follow.

Unless it was about money-and the idea that therefore Amaro had to trade Lee to be able to acquire Halladay-there was no reason to make the second trade. Even if you grant Amaro’s notion that the Phillies wanted to restock the farm system, trading Lee now wasn’t at all necessary. The Rangers, having missed out on John Lackey and having watched the Mariners getting better, could be in on a starter. The Mets are looking for rotation help. Any number of teams might have come up with a package better than what the Mariners did, and unless there was a directive to hold down the payroll by trading Lee right now, it behooved Amaro to explore those paths. There was no baseball reason to trade Lee in connection with acquiring Halladay, and no defense of doing both at the same time that doesn’t include the phrase “arbitrary payroll figure” sounds na├»ve.

The Phillies’ penury is the Mariners’ gain. With Erik Bedard making just 15 starts last season, the Mariners’ rotation consisted of a Cy Young candidate and a huge falloff to a series of fourth starters. Adding Lee to Felix Hernandez gives them a pair of starters that matches any team’s top two, and with Ian Snell, Brandon Morrow, and Ryan Rowland-Smith lining up behind those two, the Mariners’ rotation now looks like a strength. This is a team, remember, that put a tremendous defense on the field last year, and with the re-signing of Jack Wilson and import of Chone Figgins, will look to do so again in 2011. Bumping the payroll by trading for Lee and signing Figgins confirms for me a comment I made in a chat session a few weeks back: the Mariners may have decided that they won’t be able to sign Hernandez, and will instead try to win a championship in the next two seasons with him. The upgrade from the pitchers who might make the 32 starts Lee will take next season-Doug Fister, Garrett Olson, a third-tier free agent-to Lee is a standings gain of perhaps six wins, or as much of a gain as you can reasonably make in one transaction. Adding Lee moves the Mariners from a .500 team to one of the co-favorites in a division where the Angels have taken huge talent hits and the Rangers might be a year shy of asserting dominance. Depending on how the rest of the winter shakes out, the Mariners might be the team to beat come April, but they still need at least one, maybe two hitters.

They didn’t cripple their future in making this deal, either, giving up less in talent to get Lee than the Phillies did to get Halladay. Phillippe Aumont is a 2007 first-round pick who has just 106 2/3 professional innings under his belt, in part because he was converted to relief a year ago after elbow soreness plagued him in ’08. He’s basically an upside play for the Phillies, with the elbow issues and lack of a third pitch a tradeoff for the great power sinker and youth. Tyson Gillies had leadoff-man skills, with a career .419 OBP and 80/33 SB/CS numbers in three pro seasons. He draws walks and runs, and it will be interesting to see what happens to his strikeout and walk rates as he hits Double-A next year. In a package of long-term plays, Gillies is closest to the majors. Juan Ramirez, J.C. in some reports (for Juan Carlos), is all projection, no performance, advancing one level a season despite mediocre ERAs and passable rates. As Kevin Goldstein noted last month, though, “Ramirez has a big body, a big fastball, and many scouts think he’s just a few refinements away from taking off.” The Mariners traded long-term upside, players who would not be in the majors until 2012 at the earliest, to make the 2010 team as good as it can be. This trade is the strongest statement about a GM’s belief in where his team is as you’ll find; Jack Zduriencik thinks the Mariners can win this year, and that they are no longer, if they ever were, rebuilding. At that, however, the Mariners didn’t trade Brandon Morrow, they didn’t trade Michael Saunders, and they didn’t trade Carlos Truinfel. They still have building blocks for future teams.

As good as the Mariners did, though, the big winners here were the Blue Jays. Behind the eight-ball with a pitcher they could not sign and could not trade without his permission, which likely meant a value-killing contract commitment, they were able to bring in three prospects who could all be part of winning teams in the middle of the decade. What Alex Anthopolous brought back dwarfs what the Twins got for Santana two years ago. It’s too easy to say that Drabek could grow into a Halladay replacement, but he has that kind of ability. Remember that the Blue Jays have shown a facility for turning lesser pitchers into league-average starters. Drabek has more talent than any pitcher in their system. D’Arnaud is a polished hitter with a strong enough arm to remain behind the plate, and while he doesn’t have the star potential Drabek has, he projects as an inexpensive, good player at a key position.

Anthoplolous traded the third prospect, Taylor, to the A’s for Brett Wallace. This is an interesting challenge trade, dealing the more complete player for the player with one dominant skill. The Jays’ advantage in acquiring Wallace is that they will be able to develop him as a first baseman if need be, as they have only Lyle Overbay in his way, and that only for a year. Wallace isn’t as bad a third baseman as he looks to be on first glance, lacking lateral range but having acceptable hands and moving fairly well back and forth. An eventual move off of third has long been assumed inevitable, and if that is necessary, the Jays can fade that. Wallace joins Travis Snider and Adam Lind for what could end up as a championship-caliber middle of the lineup. For the A’s part, they get the player with the broader skill set who may fit their situation a bit better; the A’s need outfielders who can cover ground, and Taylor is a good right fielder who could make their team out of spring training.

All of these moves were set in motion by one decision: Roy Halladay taking half his value to pitch for the Philadelphia Phillies. For that, the Phillies assure themselves an ace in 2011-13, the Blue Jays get a package that didn’t look within their reach to kick-start their rebuilding, the Mariners launch themselves to perhaps a lead role in the AL West, and the A’s align their talent slightly better as they try to get back to prominence. That’s a big day for one man, and he won’t even throw a pitch for his new team for another two months.