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Yeah, it was related to QuickTime.

San Francisco Canyon Company was hired by Apple to port QuickTime to Windows, later it was hired by Intel to do some work on Indeo. Intel and Microsoft used the work done by San Francisco Canyon Company to jointly to improve Video for Windows performance, but San Francisco Canyon Company allegedly included QuickTime code and proprietary information without Apple's permission.

Things got nasty but Jobs opted to use this leverage to give Apple some credibility when it had suffered a serious blow from the Copland wreck.

Jobs set the terms: Apple and Microsoft agreed to cross-license each others patents, current and prospective lawsuits were dropped, Apple agreed to make IE the default browser, Microsoft agreed to continue developing Microsoft Office for Mac for 5 years and Microsoft would announce the purchase $150 million in non-voting stock.

It wasn't done out of pity, Microsoft's lawyers likely believed they would lose the case and this was a sweetheart deal which it would have been stupid to refuse.

https://en.wikipedia.org/wiki/San_Francisco_Canyon_Company

http://www.theregister.co.uk/1999/02/01/maritz_on_apple/



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