Originally written on Fangraphs  |  Last updated 4/12/12

The Twins announced Wednesday that their top starter, Scott Baker, would miss the rest of the season after upcoming surgery to clear scar tissue from his right flexor pronator tendon. While this procedure has a shorter rehab time than Tommy John surgery, the rehab process is expected to take around six months, leaving Baker unavailable until late October at the earliest. The good news for Baker is that his ulnar collateral ligament was not damaged, so he will be able to go through a normal offseason work program and should be ready for spring training. The bad news for the Twins is that their already thin rotation just lost their captain.

Baker’s elbow has been a source of increasing trouble for him over the last two seasons. He missed two weeks in 2010 with soreness, then had offseason surgery to remove bone chips, which set him back in spring training, but otherwise didn’t limit him in the first half of the 2011 season. Prior to the All-Star break, Baker was anchoring the Twins rotation with a 1.17 WHIP, a 3.01 ERA, and 104 strikeouts in 110.2 innings. After the break, he threw just 24 innings and spent nearly two months on the disabled list between two stints, both for a strained flexor tendon.

Twins officials believe that he could have pitched more at the end of the season, but didn’t feel the need to add any innings to his arm, for reasons that are certainly understandable;  the Tigers had the division well in hand and Baker’s return wasn’t going to change that. Baker was kept on his normal offseason routine — which does include a few elbow exercises — but his plan was not specifically altered to address the flexor tendon that had sidelined him.

This season’s problems for Baker started early, as he had his third spring start pushed back due to stiffness in his elbow, which — much like 2011 — was only supposed to set him back by about a week. The plan had been to start Baker in the minors, then bring him up the majors, but just 11 pitches into his first rehab outing, the stiffness came back and Baker was pulled. The team had an MRI performed, which was reviewed by Dr. David Altcheck, who determined that Baker’s repeated flexor strain would benefit from surgical intervention.

Baker’s base contract is up after this season, but includes a team option for $9.25 million. It seems somewhat unlikely that the Twins will exercise that option even if they would like to retain Baker. He’ll be coming off his second surgery on his pitching elbow and would be their third highest paid player, which is a substantial commitment to a pitcher who has never had a season above 3.5 WAR. Yes, if he were healthy, Baker could easily be a 4 WAR player, but instead he has seen his innings drop from a high of exactly 200 in 2009 to 170.1 in 2010, 134.2 in 2011, and finally 0 in 2012.

If Baker doesn’t return to the team, the Twins will turn to something resembling a youth movement to patch the hole. One of their top prospects, Kyle Gibson, comes back from Tommy John surgery this year and 23-year-old Liam Hendricks is already making a claim on a rotation spot with Baker and the newly acquired Jason Marquis both missing starts to open the season.

In the short term, the news isn’t good at all for the Twins. They’ll likely move forward with a rotation of Francisco Liriano, Carl Pavano, Nick Blackburn, Anthony Swarzak, and Hendricks until Marquis is ready, at which point either Swarzak will move to the bullpen or Hendricks will go back to the minors. 2012 was always going to something of a tough row to hoe for the Twins, but losing Baker for the full year — without having an obvious replacement in place — is a severe blow to whatever their chances might have been.

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