The fight for Skype has ended. After weeks of nasty legal sparring, the Internet telephony service’s founders agreed to join the investor group purchasing it from EBay (EBAY) and dropped the lawsuit that had threatened to bollocks the deal.

“Skype will be well positioned to move forward under new owners with ownership and control over its core technology,” said eBay chief executive John Donahoe in a statement. “We look forward to closing the deal and focusing on growing our core e-commerce and payments businesses.”

Under the terms of the agreement, Skype founders Niklas Zennström and Janus Friis will take a 14 percent stake in the company they founded and then sold to eBay, which will include an investment by them.

BoomTown’s Kara Swisher reported yesterday that the total was 13 percent–10 percent for the rights to key Skype technology held by the founders and the option to invest $83 million for three percent more.

In exchange, the pair will give Skype software essential to its operation and drop their various lawsuits against eBay and Skype buyers.

Interestingly, Index Ventures, which helped orchestrate the deal, is leaving the consortium of investors taking a majority stake in the company–as BoomTown reported earlier this week. Index partner Michelangelo Volpi, a former employee of Skype’s founders, had been at the center of one the suits that threatened to ruin the deal. Said Index partner Danny Rimer: “The deal terms changed for Index such that it no longer matches our investment criteria and thus we have decided not to participate in the transaction.”

PREVIOUSLY:

• Volpi and Index Ventures Out of Skype Deal, the Lawsuit-Happy Founder Twins In
• I Love the Smell of Settlement in the Morning: Skype Founders Set to Get 10 Percent, Option to Buy Three Percent More and Two Board Seats
• Volpi and Index Smack Back at Skype Founders With Motion to Dismiss (Plus Filings!)
• When Entrepreneurs Attack! All 10 New Skype Lawsuit Filings!
• Dueling Skype Sides Hire Big Communications Guns
• Skype Actually a “Voice Over IP Litigation” Service

And now this: eBay’s plans to spin off Skype next year are being threatened by a legal dispute over the telephony service’s underlying technology.

In a 10-Q regulatory filing Thursday, the online auctioneer said it is developing an alternative to that technology, which it licenses from Joltid, a company run by Skype co-founders Niklas Zennstrom and Janus Friis, but there is no guarantee of success. And if it fails in that effort and its legal dispute with Joltid drags on, eBay could be forced to shutter Skype.

“Although Skype is confident of its legal position, as with any litigation, there is the possibility of an adverse result if the matter is not resolved through negotiation,” the company said. “Skype has begun to develop alternative software to that licensed through Joltid. However, such software development may not be successful, may result in loss of functionality or customers even if successful, and will in any event be expensive. If Skype was to lose the right to use the Joltid software as the result of the litigation, and if alternative software was not available, Skype would be severely and adversely affected and the continued operation of Skype’s business as currently conducted would likely not be possible.”

That doesn’t bode well for eBay’s plans to take Skype public in the first half of 2010. Though the company insists its plans to separate the telephony service have not changed, it’s clear that eBay (EBAY) must resolve these issues before moving ahead.

Certainly, it will be difficult to gin up investor interest in an IPO for a disabled service run by a company that spent billions of dollars to purchase it and failed to secure its underlying technology.

Some people have been critical of Skype, but I am very proud of the company’s growth. Very few companies can claim to match the growth trajectory Skype is on and continues to be on.”

Skype co-founder Niklas ‘NZennström’

It’s taken two years longer than it should have, but skepticism with which investors met eBay’s $2.6 billion-plus purchase of Skype in October 2005 has finally made its way up to eBay management.

This morning the Internet auction giant said it was taking a $1.43 billion charge for its acquisition of the Internet telephone provider and that Niklas Zennström, a co-founder of Skype, was stepping down as chief executive of the division. The charge announced today reflects the “updated long-term financial outlook for Skype,” eBay said in a filing with the Securities and Exchange Commission.

Though Skype’s membership and revenues have grown since the acquisition, it has fallen far short of Wall Street’s general expectations for it. And try as it might, eBay just hasn’t been able to figure out a way to make the sort of money it needs from the company to justify that astonishing $2.6 billion purchase price. Said Derek Brown, an analyst at Cantor Fitzgerald, “It has seemed relatively clear that Skype has underperformed even modest expectations for the last two years.”

Silicon Alley Insider’s Henry Blodget agrees. “The Skype acquisition never made sense strategically, and one reason Skype has struggled, we think, is that it is just a distraction to eBay (which needs desperately to focus on its core commerce business),” Blodget writes. “eBay should immediately sell what’s left of Skype to Yahoo, Microsoft, or Google, all companies that offer portfolios of communications services that Skype might actually benefit from being a part of. Skype is rapidly surrendering its early dominance of soft-phone VOIP to other more focused competitors, and if it stays within the eBay fold, we think further write-downs will be in the offing. Skype was a $2 billion to $4 billion eBay Hail-Mary pass, and it just officially fell incomplete.”