Since Destiny 2 is moving away from Battle.net, will it automatically uninstall on Shadowkeep's launch?
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At this time, there's been no mention of a transfer system in place, and along with that, there's been no mention of an auto-removal of the already-installed version from the Blizzard Battle.net launcher. Without such being announced, you'll need to uninstall the Blizzard version yourself and install the Steam version yourself.