I have noticed that many people seem to be playing Run 2 in a web browser or a bad flash game player. (eg. Firefox, Like i used to) Playing on these platforms makes the game laggier and slower, which can make you lose 1-15 seconds in a run depending on the website or flash player.
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The fastest and smoothest way (found so far, by DHA, ty) to play Run 2 is with adobe flash player 11, found here- http://www.flashflashrevolution.com/vbz/showthread.php?t=120256 Scroll down till you see the downloads for each platform and get the correct one.
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Obtain the .swf file of run 2 either by getting it from kongregate/coolmath yourself (look up a tutorial if you want to do it this way) or just downloading it from someone who already has. I got mine here- https://sites.google.com/site/baroneflash/run-2
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Next, open the flash player, drag the .swf file into it, and you will be playing run 2!