As HoSpanky and Peter M Smith indicated there are enemies. They are configurable just like the resources for how often they appear and how big their bases are -- as well as the options to make them "peaceful" they only attack you when you attack them or to eliminate them completely. In early versions you needed items you received from killing them for some late game items. That's no longer the case.
Their very presence is a bit of a philosophical argument among the community. It does fit the "story" of the game and does provide some additional challenges/obstacles. However many feel the game is about building and designing your base/factory, not fighting aliens. In the early game they can be dangerous. However unless you have cranked up their numbers in the beginning configuration, by mid game they are not too much of a bother. In the end game, they are nothing more than an annoyance.
Personally, I've played long games both with and without enemies. Go with whichever option sounds better to you. If you do play with them, I suggest configuring the game with a large starting area to give you some breathing room at the start of the game. Don't delay your turret research too long...
“Extinction is the rule. Survival is the exception.” -- Carl Sagan