Part of your upgrade probably involves converting the all the NTEXT columns in the Moodle database to NVARCHAR(MAX) - that was one of the changes introduced in Moodle 2.6. So, depending on how much data you have in your Moodle database, the upgrade can take a long time. To allow for that you need to set your PHP (php.ini) and IIS timeout settings to very high values so that IIS doesn't time out while the database conversion is happening in the background.
I suppose the Moodle installer should flush a "in progress" message back to the browser on a regular basis while that conversion is happening so that timeouts don't happen and you can see that things are still happening, but I guess it's too late to fix that...