While clearly glad to have its court battle with NTP over, Research In Motion ( RIMM) is leaving the scuffle bloodied and battered. Whether -- and how quickly -- the company will recover are likely the key questions facing the BlackBerry email provider -- and its stock.

The company's most noticeable and immediate injuries were the $612.5 million it paid to settle the dispute with NTP, the disappointing fourth-quarter numbers it now expects to report and slowing subscriber growth . But the case could have a longer-lasting effect by giving a boost to rivals who stayed out of the fray with NTP.

On a conference call Friday afternoon, RIM officials tried to reassure the market that the company wouldn't spend long convalescing. Customers cut back on their deployments of BlackBerry systems in recent months when a court-ordered injunction against the system looked like a distinct possibility, acknowledged co-CEO Jim Balsillie on the call. But no carrier or customer cut ties with RIM as a result of the legal dispute, he said. Meanwhile, the company expects to announce a "raft" of new partnerships in coming months, he said.

"Our opportunities and prospects are orders of magnitude greater than the settlement amount ," said Balsillie.

And at least initially, the market seemed to react more with relief that the fight with NTP was finally over than any concern over RIM's future health. In after-hours trading following word of the deal Friday, RIM's stock surged more than 20%, before cooling slightly.

But at least some investors were already betting that RIM's victory in ending the battle with NTP was a Pyrrhic one. The legal dispute was always "smoke and mirrors," says David Schamens, a portfolio manager for Charlotte, N.C.-based Invictus Funds, which has less than $100 million under management. Now that the battle's over, RIM will have to face up to the real fight on its hands: competition from the likes of Microsoft ( MSFT), he says.

New high-speed wireless phone technology poses a distinct threat to RIM's core business of delivering email instantly to mobile devices, Schamens says. If that happens, RIM becomes nothing more than a handset manufacturer subject to the intense competition and commoditization of that market, he says.

"Within a year, I see more and more people switching from RIM," says Schamens, who shorted RIM's stock after its post-settlement rise on Friday.

Whatever the longer-term outlook, the dispute with NTP has clearly left its mark on RIM.

The settlement amount, for instance, represents more than a third of the $1.8 billion in total cash and investments RIM held on Nov. 26 at the end of its last fiscal quarter. It also is more than one-third larger than the $450 million RIM would have had to pay under a previous settlement agreement that fell apart last June.

Of course, the market was expecting a lot more; some analysts forecast RIM would have to pay $1 billion or more to finally make the case go away. But even if the dent in the company's balance sheet wasn't as big as was feared, the drop in cash will likely weigh on the company's future earnings expectations -- and potentially its share price.

During the first nine months of this fiscal year, the company hauled in roughly $47 million in investment income on its cash, which works out to be about 18 cents a share after taxes. Overall, the company posted $1.84 a share in earnings over the first three quarters of this fiscal year.

But perhaps more troubling than the cash outlay is the effect the NTP fight has had on RIM's underlying business. Apparently lost amid Wall Street's celebration of the settlement announcement on Friday was a separate report from the company warning that fourth-quarter results will come in far shy of analysts' expectations. Not including the settlement amount, the company now expects to earn 64 cents to 66 cents a share on sales ranging from $550 million to $560 million in the quarter ending March 4.

In contrast, Wall Street was looking for a profit of 78 cents a share on sales of $608.6 million. The company had previously predicted it would earn 76 cents to 81 cents a share on sales of $590 million to $620 million in the quarter.

In a statement, the company blamed the shortfall on the "uncertainty" in the market relating to its dispute with NTP.

But the results of that uncertainty could last longer than just this one quarter. For the third quarter in a row, RIM also warned that additions to its subscriber base would come in lower than it previously forecast. Indeed, Friday's warning marked the third time that the company has lowered expectations for subscriber growth for the current quarter alone.

The company now expects to add 620,000 to 630,000 subscribers to its BlackBerry service in the current quarter. Its initial guidance for the quarter, given last year, had called for the addition of 775,000 to 825,000 subscribers in the quarter.

That shortfall could well have implications on service and hardware revenue in coming quarters and force analysts to bring down their earnings expectations even further.

And those are just the known injuries. Given the company's weakened state, investors such as Schamens are betting that rivals could inflict even more pain on the company in coming quarters.

While the market for technology that can deliver mobile email may be a big one, the market for BlackBerry-style pagers -- RIM's core hardware -- is a limited one, he argues. And with Microsoft now setting its sights on that market with the latest version of Exchange e-mail server software, RIM has a very dangerous competitor, he says.

"Those two factors will ultimately spell trouble for RIM," he says.