By Katie Benner
May 26, 2011

First Microsoft, now the Mets. The Greenlight Capital founder is supporting the teams that no one loves. 

FORTUNE — This year, David Einhorn is throwing his money behind the underdog.

By the end of next month, the founder of hedge fund Greenlight Capital will trade $200 million for a minority stake in the New York Mets, the Major League Baseball team that lives in the shadow of the Yankees and that has missed the playoffs for four years in a row.

Let’s just assume that the man who was smart enough to short Lehman Brothers is doing this all for love.

But what are we to make of Einhorn’s long position in Microsoft (MSFT)? The tech company has floundered for a decade. It missed tech shifts like the rise of the smart phone, the move back to the data center, and the virtualization of software. And Microsoft doesn’t have a portfolio that makes sense in the new world. The company’s market cap has been cut in half since its 1999 peak; and with the stock stuck at around $25 investors are about as fed up with Mr. Softee as fans are with Mr. Met. (I kid, no one could ever tire of their favorite sniper).

Einhorn’s endorsement of Microsoft (it’s a value stock!) comes with a giant string attached: the board must fire chief executive Steve Ballmer. And so Einhorn, the man who made his name as a short seller and all around agitator of companies doing bad things, is hedging into activist investor territory.

Fortune wrote this March that “the root of Microsoft’s paralysis seems to be Ballmer himself,” basing this claim on interviews with former Microsoft executives who believe that Ballmer is determined to keep Microsoft frozen in time, making money off of the legacy businesses he inherited from Bill Gates.

If this is the case, then someone has to hit control-alt-delete; and Einhorn is ready to take on the job. But the hedge fund manager has his work cut out for him. The company’s largest shareholders include Ballmer and Gates, and the board has thus far not shown much interest in agitating for change.

As we’ve seen with Allied Capital and Lehman, it’s not a good idea to underestimate Einhorn in a fight. Mets fans take note. If he can do something about Ballmer, maybe Jason Bay is next…

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