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Just when i thought i was done with this game, i find there's a secret level in it. You sir, are a genius, and have made 30 minutes of my summer seem smart. At least there's not a secret square in the secret level. (Right?)
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I feel like I was just trained to be a monkey hacker by the scientist's cat.
And I agree with "attacked with a tire iron."
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The stages for the secret squares mentioned by SpectralFlame are: Mod_A - 5 Mod_B - 4 Mod_C - 5 Main - 5 Dir - 7 Sys - 1. How to get them is kind of tricky, but now you have a guideline.
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The end says "Thank you, organism" which leads me to think that I was just put through a situation similar to how animals feel when being tested on. They do what they are told, and get a reward (in this case a banana). Nicely done :)
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I think the test subject hacked into the server and killed itself. Or, uploaded its consciousness to the Net. Either way, good minimal story.