I'm currently running El Capitan on a Macbook Pro mid-2015 model and just can't seem to upgrade to Sierra. Every time I try to download the installer from the app store, it completes, says 'Downloaded' but it's nowhere to be found. I watch Finder during the download and a partial appears under Applications called 'macOS Sierra'. When the download completes another file appears in its place called 'Install macOS Sierra' but that file then immediately disappears!
I've been unable to find anyone else with this issue and it seems to be impossible to manually download the installer so I can run it without the App Store deciding to delete it.