In most books you have the bad guys and the good guys, but what I've found in quite a lot of SciFi stories is that the government is always the bad guy.
If you want your story to be different to everyone else's try to make your 'bad guy' someone that you wouldn't expect. Someone that the reader is lead to believe is good.
I suppose a lot of what writing is about is coming up with new ideas, ones that may surprise people. Nobody wants to read hundreds of the same book! So when writing about bad guys, use someone other than the government.
HOWEVER
If your bad guy is a monster/alien/non human you may have some other issues.
You need to fully describe this enemy, and then describe why they are the 'bad guys'. You can't just assume that the reader will get it because you do, you have to clarify everything and make sure things are clear :)
-E
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How To: Write SciFi
No FicciónScience Fiction is that genre that is full of mystifying, magical, sometimes terrifying stories. It allows you to enter a new world, one which is almost unrecognizable to the one you live in. We all know which books have encaptured our imagination...