Traditionally, the end of an era is marked by terrible portents and cataclysmic events. As signs go, the sight of Sun's Scott McNealy exchanging banter (and hockey shirts) with Microsoft's Steve Ballmer might seem mild enough, but the shift it represents is indeed epochal.

The two companies come from very different backgrounds: Microsoft grew from the world of the first personal computers, Sun from workstations. But as their ambitions overlapped in the networked business world, Scott McNealy's strategy has been increasingly defined by his fierce and vocal opposition to Microsoft, especially once the latter took over from IBM as the driving force in computing.

This makes the cosying-up of the two companies extraordinary, even if the benefits of doing so are clear. Sun gets a couple of billion dollars, while Microsoft removes another troublesome competitor – one that had a dangerous tendency to call on national governments for help in its legal battles.

But most of all, both can take comfort from the creation of a united front against a common threat: GNU/Linux. Steve Ballmer gave the game away when he explained at the press conference where the Sun deal was announced that “it's an agreement that comes from two companies that believe in intellectual property, that develop intellectual property and that are respecting intellectual property.”

The hammering home of the “intellectual property” mantra emphasises how this forms the cornerstone of Microsoft's latest attempt to tame the free software tiger. Previous approaches included trying to demonstrate technical superiority and, claiming that the total cost of ownership (TCO) was higher for GNU/Linux.

Stemming the rising tide of the open source operating system is vital for Sun, too. For some years it has taken the line that its own high-end Solaris can co-exist quite happily with low-end GNU/Linux. But with the release of version 2.6 of Linux, which scales to 32 processors, this position is no longer tenable.

Sun's ambivalence in this area has become even more evident recently in the wake of various calls to make Solaris and Java open source. Supporters of such moves argue that doing so would make them more widely used. In the case of Java, Sun counters – with some justice – that making it open source would be likely to lead to fragmentation, which would undermine its key feature: “write once, run anywhere”. Indeed, one of Sun's most protracted legal battles with Microsoft was over precisely this issue. Sun's victory on that occasion may have been one reason why Microsoft decided to buy a little peace.

The situation for Solaris is in some ways more straightforward. Since it will inevitably be overtaken by GNU/Linux, it is hardly worth devoting too many resources to its further development. Better to let the open source community take it over and to do it for free.

This would leave Sun as essentially a Java company. Scott McNealy already seems to be nudging Sun in that direction: in a recent speech he emphasised the vigour of the Java world, and its bright future in new areas like gaming. Moreover, the success of the Java Desktop offers a way to work with rather than against GNU/Linux without even having to use the “L” word.

The Sun-Microsoft rapprochement marks a reining-in of a major independent player that has played an important role in the world of computing. Despite the considerable cash generated by the deal, Sun still finds itself in a difficult position strategically. It would be ironic if Sun went down in history chiefly for its generous contributions of code to the open source world, beginning with StarOffice – a move designed to damage Microsoft - and perhaps culminating with Solaris and Java.

Glyn Moody welcomes your comments.