I notice the comments saying that the manual retreat and manual acts of gods are "bad" I think if it were not that way the game would be too easy. For me it makes me feel more hurried more like I am in a fray plus only two of em are manual the other 3 are press and forget.
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Usually if the game won't save, the problem is your browser blocking third-party cookies. Are you using Safari or any privacy-related browser extensions? Make sure "www.swarmsim.com" has permission to set cookies (localstorage).