The Astros did not sign number one overall pick Brady Aiken. This is a big deal.

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The signing deadline for players selected in this year’s Rule 4 draft came and went at 5PM Eastern. And the number one overall pick, Brady Aiken, did not sign with the Houston Astros, reports Jim Callis of MLB.com.

If you aren’t up to speed, the Astros selected Aiken with the first overall pick and the parties agreed to a $6.5 million bonus in early June. But following a physical on June 23, the Astros became concerned about something in his left elbow and subsequently offered Aiken $3,168,840. Aiken’s agent, Casey Close, lashed out at the Astros, saying there was nothing wrong with Aiken and the Astros were trying to play hardball in an effort to manipulate their bonus pool to sign other players. Tony Clark of the MLBPA waded in to the controversy as well, saying on Tuesday that he was “disappointed” in how the Astros were dealing with Aiken.

Moments ago, following Callis’ report, Astros GM Jeff Luhnow told Evan Drellich of the Houston Chronicle that “[w]e tried to engage Casey Close three times today … there was no interest.”

The technical fallout: Aiken now has a choice: he can attend UCLA (assuming his dealings with close don’t burn his eligibility), and not be eligible for the draft until 2017. Or, he can play at a junior college or in an independent league and be eligible for the 2015 draft. From the Astros side, since their offer to Aiken was at least 40% of the his slot value (it was exactly that, actually) they will be given the number two overall pick in next year’s draft as compensation in addition to whatever pick they have.

The practical fallout for Aiken: he has to wait a year or maybe three to cash in and when he does it’s unlikely that he’ll do as well as he was set to do this year. And many, depending on how much stock they put in the Astros’ word on Aiken’s health, may consider him damaged goods.

The practical fallout for the Astros, they will be without a top pick. This, a year after their 2013 top pick, Mark Appel, has struggled mightily. More significantly, they may have their reputation among agents and future draft picks substantially damaged. Of course, it’s also the case that we don’t know — and likely can’t know due to confidentiality concerns — what the Astros saw in Aiken’s elbow. If it was legitimately serious, well, maybe they’re just being prudent. At the same time, Casey Close is not a bomb-thrower, and his reaction to all of this was pretty sharp. That he is as angry with the team as he has been suggests some seriously toxic dealings between the parties that many may read in his favor and negatively toward the Astros.

Ultimately, though, this blew up and there will likely be some heavy consequences for both sides. All over a tad north of $3 million, which is less than the Houston Astros are paying Jose Veras this year.

Jim Crane thought the heat over sign-stealing would blow over by spring training

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The Astros’ sign-stealing story broke in November, a steady drumbeat of coverage of it lasted through December and into January, when Rob Manfred’s report came out about it. The report was damning and, in its wake, Houston’s manager and general manger were both suspended and then fired.

After that a steady stream of media reports came out which not only made the whole affair seem even worse than Manfred’s report suggested, but which also suggested that, on some level, Major League Baseball had bungled it all and it was even worse than it had first seemed.

Rather than Manfred and the Astros putting this all behind them, the story grew. As it grew, both the Red Sox and Mets fired their managers and, in a few isolated media appearances, Astros’ players seemed ill-prepared for questions on it all. Once spring training began the Astros made even worse public appearances and, for the past week and change, each day has given us a new player or three angrily speaking out about how mad they are at the Astros and how poorly they’ve handled all of this.

Why have they handled it so poorly? As always, look to poor leadership:

Guess not.

In other news, Crane was — and I am not making this up — recently named the Houston Sports Executive of the Year. An award he has totally, totally earned, right?