Before we get into the weeds, try the simplest solution. Right-click your desktop, launch Steam as , then launch Prototype 2 . Play for five minutes, trigger an auto-save, then exit. Does it work? If yes, the issue was permissions. You can permanently set steam.exe and Prototype2.exe to "Run as Administrator" in their properties menu.
The game expects saves in:
To prevent similar issues in future prototypes, the following measures are recommended: prototype 2 failed to save data fix
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Have a fix I missed? Did the registry trick work for you? Let me know in the comments below. Keep evolving. Before we get into the weeds, try the simplest solution