The battle between Sun and Microsoft over inclusion of the Java Runtime Environment (JRE) in Windows wages on. At stake, according to a U.S. District Court, is the fairness of the fight between Java and .Net. for middleware supremacy.

Court documents indicate that unless certain legal measures are taken to level the playing field, Microsoft's monopoly of the Intel-based desktop operating system market --- and the distribution channel that monopoly represents --- could lead to another monopoly of the middleware market.

In other words, if .Net is distributed with Windows and Java isn't, .Net could end up reigning supreme over Java because of its market clout rather than based on the merits of the platform versus Java. Should that hypothetical scenario ever become reality, many businesses that have already decided on Java as their strategic middleware platform could eventually find themselves paying dearly. On behalf of the American public, antitrust law attempts to prevent market injustices of this nature.

Depending on the outcome of this case --- which is far from over --- you may have to consider the long term odds of either platform's success before making a strategic decision today.

Representing Sun is Richard Green, vice president of developer tools. In explaining Sun's case to me, Green focused on a little-known finding in the recently ordered preliminary injunction that deals with copyright infringement.

According to Green, Microsoft's license to distribute the JRE with Windows required more of Microsoft than simply to distribute a 100 percent Java Community Process (JCP)-compliant version of the JRE. Green said Sun's copyright and license -- better known in the context of this case as the Technology License and Distribution Agreement (TLDA)--were carefully worded to insure that the JRE was physically installed on all systems that came pre-installed with Windows.

"In other words," said Green, "when Windows XP first shipped without a [JRE] and Microsoft forced users to download the [JRE] from its Web site the first time it was needed (to run some Java code), that method of distribution was in violation of the copyright."

The text from the injunction does cite Sun's motion for a copyright infringement. Against the backdrop of a deliberation over the meaning of the word "incorporation" (as in "incorporation of the JRE into Windows"), the opinion appears to legitimize Sun's complaint that any means of distribution other than including a JCP-compliant version of the JRE as part of installations of Windows is not enough.

Microsoft spokesperson Jim Desler said his company has been on a path to discontinue any support for its own JVM and support Sun's version, but now wants to rid itself of dealing with Java.

"We were already on a path to issue Service Pack 1a for Windows XP," Desler said. "That service pack, which was announced last week, is part of our continuing effort to phase out support for Microsoft's Java Virtual Machine (JVM)--a phase out that's contemplated as part of our prior settlement with Sun in 2001. The only difference between Service Pack 1 and Service Pack 1a is that 1a doesn't have our JVM and Service Pack 1 did. But as a result of the preliminary injunction, we were on a path to release Service Pack 1b, which was to include Sun's JRE. Right now, we're moving forward with 1a. Our goal is to get out of the Java business in a way minimizes the hardship to our customers and in a way that we can still support them."

Unfortunately for Sun, Microsoft's plans for Service Pack 1b with support for Sun's JRE are now on hold. Microsoft's appeal resulted in a stay of the preliminary injunction by the 4th Circuit Court of Appeals, pending yet another hearing. That cleared the way for Microsoft to hold off on distributing Sun's JRE -- for now. But Green remains confident that Sun will prevail.

"When it's over," said Green, "Microsoft will have to distribute the JVM to existing Windows XP users via all of Microsoft's upgrade channels including CD-ROM and the Internet-based Windows Update feature. All new copies and installations of Windows XP and any future version of the desktop version of Windows will have the JVM included by default."

Desler countered Green's position as part of an overly broad set of claims. "Green is free to look into his crystal ball," Desler said. "We feel that Sun's claims have no merits, and it will be decided in due course in the courts."

If Sun were to emerge victorious on the copyright infringement issue, the company could pursue damages. In the section that addresses the copyright issue, the original injunction states that "Sun is entitled to the presumption of irreparable harm." Green responded that Sun was "undecided on this point."

Green also implicated the systems manufacturers who distribute Windows with their hardware as unknowing participants with Microsoft in the alleged copyright infringement. He said that Sun had advised the systems manufacturers of the situation. Though stopping short of saying that the manufacturers broke the rules, Green made it clear that the manufacturers may need to spend more time examining the license agreements of the software companies with which they do business.

I asked Green to clarify what he meant about advising the systems manufacturers of the potential legal exposure. For example, were the manufacturers formally notified with a letter from Sun's legal department? "No," said Green. "It's a small world. We know each other. It wasn't that formal. We just contacted them." Green acknowledged that suing the manufacturers could backfire from a public relations perspective. He didn't think Sun would take that course of action.

With all this litigation and legal wrangling, it's useful to look back to the Appellate Court's June 2001 opinion on District Court Judge Thomas Penfield-Jackson original ruling and break up remedy against Microsoft.

Citing practical difficulties in remedying monopolistic behavior when market dynamism may render the remedy irrelevant by the time it's implemented, the Appellate Court wrote, "By the time a court can assess liability, firms, products, and the marketplace are likely to have changed dramatically. This, in turn, threatens enormous practical difficulties for courts considering the appropriate measure of relief in equitable enforcement actions, both in crafting injunctive remedies in the first instance, and reviewing those remedies in the second. Conduct remedies may be unavailing in such cases, because innovation to a large degree has already rendered the anticompetitive conduct obsolete (although by no means harmless). And broader structural remedies present their own set of problems, including how a court goes about restoring competition to a dramatically changed and constantly changing marketplace."

In this industry, the same seems to hold true of any court order, injunction, or action that drags on. Green doesn't believe that Sun's window of opportunity to recover from any alleged damage is in danger of closing soon. "For now, it's still open and we think it will be for quite a while," Green said.

Green's definition of "quite a while" will have to be quite liberal. Judging by the way things have dragged on so far, resolving the JRE controversy could take years. Unfortunately for Sun, for every copy of Windows XP that doesn't ship with Sun's JRE, the window of opportunity that the preliminary injunction attempted to prop open closes a just little bit more.

As a part of an attempt to guarantee a competitive middleware market (aka: Java vs. .Net), should Microsoft be forced to distribute Sun's JRE with every copy of Windows? Or, do you think the courts are overestimating the effect of the Windows "distribution channel" on the battle between Java and .Net? Use ZDNet's TalkBack to debate the issue with your fellow readers or write to me at david.berlind@cnet.com.