Bill Ackman sure does like struggling retail operations. He's an activist investor, and he invests with the belief that he will be able to help the company by pressuring management into new strategies or pressuring the board into finding new management.

Ackman is at it again, as news came out on Friday -- and Thursday for insiders (just look at the late day chart of the stock) -- that his hedge fund, Pershing Square Capital Management, had acquired a 16.5% stake in J.C. Penney (NYSE: JCP). A regulatory filing disclosed on Friday showed that Ackman beneficially owns 39 million common shares. A separate filing also showed Ackman held a 10.9% stake in Fortune Brands (NYSE: FO).

It looks like Ackman is also going to be a pretty active investor in J.C. Penney. He announced in the filing that Pershing Square plans on actively engaging with management on matters related to the business, including its assets and current financial condition.

The Target fall-out
J.C. Penney isn't the only underperforming retailer in which Ackman has tried to unlock greater returns for its shareholders.  Earlier this year, he sold his stake in Sears Canada to Sears Holdings (Nasdaq: SHLD), and he still has a large position in Borders Group (NYSE: BGP). However, Ackman's biggest bet in recent years was with Target (NYSE: TGT), which has been an ongoing battle.

Ackman dedicated his entire Pershing Square IV fund to his Target position. After making Target his largest holding, he lobbied a plan to management to spin off the company's vast real estate holdings into a real estate investment trust in order to unlock the true value of the assets. When management indicated that it wanted no part in this unlocking of value, Ackman launched a bitter and expensive proxy fight against the company in order to win representation on the company's board of directors. The battle cost the company more than $11 million to defend itself.

The experience was also costly for Ackman, both in monetary terms and in lost pride. The Target position has been a drag on an otherwise stellar investment career. Reuters analyst Felix Salmon calculated that at the end of 2007, the year Ackman initiated the position, the Target fund lost more than $850 million. As of June, Target was still Ackman's largest holding, representing 29% of Pershing Capital's portfolio. But with the recent additions to the portfolio, it seems likely that Ackman may wind down his Target position.

Want to join Ackman?
Ackman seems to have learned his lesson from the Target debacle. As he put it, "The investment business is about being confident enough to know that you're right and everyone else is wrong. Yet you have to be humble enough that you recognize when you've made a mistake. Earlier in my career, I think I had the confidence part pretty solid. But the humbleness part I had to learn.''

So one would expect Ackman to be more prudent in his actions and the way he works with company management. J.C. Penney has had a magnificent run up over the last month, rising more than 60% since the beginning of September. Yet with the retailer having faced falling market share due to competitors Macy's (NYSE: M) and Dillard's (NYSE: DDS), it's clear shareholders are banking on Ackman to turn things around.

Investors are always smart to focus first and foremost on the fundamentals of a company. Here, though, understanding the risks of who's investing in your company is equally important.

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Andrew Bond owns no shares in the companies listed. Fortune Brands is a Motley Fool Stock Advisor recommendation. Try any of our Foolish newsletters today, free for 30 days. The Fool has a disclosure policy.