NetApp’s deal to acquire deduplication leader Data Domain took two weeks, from start to finish, to mead out. Now, it appears that what seemed like a done deal will take weeks—if not months—to sort through.

Just two weeks ago, NetApp was celebrating its proposed union with Data Domain in a cash-stock deal worth $1.5 billion. Now that deal is in question following EMC’s unsolicited bid of $1.8 billion cash. NetApp has countered, raising its offer to $1.9 billion, in what could turn into a bidding war.

The escalating bids have some analysts and industry observers questioning the process in which NetApp originally came to terms to buy Data Domain, a specialist in deduplication technology. Given that EMC raised the stakes and NetApp quickly countered, some people question whether Data Domain did enough due diligence before signing up with NetApp.

There is no doubt the original NetApp deal happened quickly. At an impromptu town hall with partners on May 20—the day following the Data Domain deal, NetApp CEO Dan Warmenhoven recounted the process and motivation for buying Data Domain. From start to finish, the negotiations took less than two weeks and involved no more than a handful of people, he said.

Frank Slootman, president and CEO of Data Domain, did not participate in the town hall discussion. However, he was on the NetApp campus earlier that day to mark the acquisition announcement. Warmenhoven described Slootman to partners as very competitive and not a fan of EMC.

“[Slootman] realized if he didn’t do something dramatic, he wouldn’t be able to stay in the race. It struck him that EMC was gaining ground because of its global coverage,” recounted Warmenhoven as one of the reasons Data Domain sold to NetApp.

Taking on EMC as a combined entity may have been the goal of NetApp and Data Domain, but EMC had other plans. Just when it appeared as though the deal would clear regulatory review, EMC unveiled its surprise bid.

“The combination of EMC and Data Domain technologies will strengthen EMC’s leadership in the fast-growing and very important next-generation disk-based backup and archive market, and will also result in a business larger than a billion dollars for EMC in 2010,” said EMC CEO Joe Tucci in a statement.

Insiders at NetApp say the undercutting EMC bid on June 2 sent NetApp into a tailspin and scrambling to find a response. Less than 24 hours later, NetApp responded in kind with a new offer: $1.9 billion – or roughly five-times Data Domain’s annual gross income.

In a statement announcing the new offer, Warmenhoven spoke about the common cultures of NetApp and Data Domain. It was a point he made at the May 20 town hall, stating that the company has conducted several competitive hires between each other.

"The cultural compatibility between Data Domain and?NetApp will maximize the potential for continued innovation from a?creative and motivated employee base. This will not only create a?meaningful choice for our customers but also lead to a complementary combination with no obstacles to an expeditious close of the" acquisition. Therefore, we are as committed to this partnership now as we were when we first announced our intent to acquire Data Domain,” Warmenhoven said in his statement.

As of this writing, NetApp and Data Domain had notices on their homepages about their union. Data Domain’s site has no mention of EMC, but EMC’s homepage sports a notice of its offer that includes the Data Domain logo. The bottom line: it will take more than two weeks to unravel this multi-billion-dollar quagmire.