Apple had already dropped sharply twice on Tuesday — once at 10 a.m. and again at 3:25 p.m. — when, 12 minutes before the close, the volume of trading suddenly spiked and the stock went into freefall.

More than 3.5 million shares changed hands in a fury of last-minute trading, and when the dust cleared, Apple had fallen 5.27 points (2.6%) for the day to close at $196.97. Nearly 3 of those points were lost in the final 12 minutes, when $2.66 billion of the company’s market capitalization evaporated in less time than it takes to drink a latte.

What happened? That’s for the SEC to determine, assuming they care. But investors were deeply suspicious. In a day when the Dow climbed more than 126 points, there was no news bad enough to trigger a raid on Apple, no downgrades or negative analyst reports.

There was, however, some interesting back-channel chatter on the finance boards and among hedge fund managers. A partial timeline:

• 3:24 p.m. A message posted on Yahoo Finance’s AAPL board mentions a “potential UBS downgrade”
• 3:26 p.m. Another Yahoo rumor, this one that Piper Jaffray’s Gene Munster, a long-time Apple bull, is set to downgrade the stock this week.
• 3:28 p.m. TheStreet carries a brief note from hedge fund Manager Timothy Collins that reads in full: “Call me crazy, but I think Apple (AAPL) actually tests $195 (give or take a few cents). I will be a buyer on any bounce off that level, but I am holding off buying here. Just food for thought.”
• 3:48 p.m. Yet another Yahoo Finance post, since deleted by Yahoo, claims that Apple is recalling large numbers of iPhones due to battery problems.

There’s plenty more where that came from, including rumors that Steve Jobs needs another organ and that Apple’s Cyber Monday sales were terrible. (In fact, traffic at its online store was up 39% year over year on Black Friday and 71% on Cyber Monday; see here.)

Yahoo Finance’s chat rooms, of course, are notorious breeding grounds for disinformation, a place where day traders toss around rumors and insults in cryptic messages that are impossible to trace. It’s unlikely, however, that any of the participants in this game have holdings deep enough to move a few million shares.

Timothy Collins, however, is in a different league. He’s a hedge fund manager who writes for a website started by Mad Money’s Jim Cramer, a man with a long history with Apple (see here and here). Reached on Wednesday morning, Collins denied having a hand in triggering a run on Apple.

“Though I am flattered that Apple investors think I have that much influence,” he wrote, “it does give me a chuckle.  I think the reason for the stock drop had more to do with a piece at 2.50pm EST. [Here he inserts a link to an AppleInsider story about speculation that the iPhone is going next to T-Mobile, not Verizon.]”

Piper Jaffray’s Munster, for his part, dismisses the possibility that this or any other Apple story was the catalyst for the raid. “In my opinion investors were stretching for reasons,” he told the Wall Street Journal‘s Matt Phillips. “My take, there was a big seller for who knows what reason. People got worried they were missing something, and the stock tumbled.”

One more note: Bloomberg reported Monday that since August, hedge funds have been “shoveling money into stocks as individuals exit at the fastest rate in a year.” The funds’ most popular stocks, according to Goldman Sachs’s survey of regulatory filings: Pfizer (PFE), Bank of America (BAC) and Apple.

“Yes, hedge funds are buying stocks,” Morgan Creek Capital Management’s Mark Yusko told Bloomberg. “But they’re also shorting stocks in record numbers and buying put options in record levels.”

Apple shares bounced back in after-hours trading Tuesday and opened higher on Wednesday. By midmorning, shares were going for $201.23, up 4.26 points (2.1%) from Tuesday’s close. By the end of the day, however, Apple was back down to $196.23.

It also ended the day in the No. 1 spot on the Wall Street Journal‘s “Buy on Weakness” list. See here.

[Follow Philip Elmer-DeWitt on Twitter @philiped]