Atrocities comprise a set of particularly heinous acts forbidden under the Unity mission's U.N. Charter. Simple Atrocities include use of nerve gas or genetic warfare, nerve stapling of civilians, and attacks against civilian populations (e.g. intentional obliteration of a base). Use of quasi-nuclear devices such as Planet Busters is considered a Major Atrocity.
If you commit a Simple Atrocity, the other factions will likely impose commerce sanctions for ten or more years, depriving you of all trade with your Treaty and Pact partners. The faction against whom you commited the atrocity will probably remain your sworn enemy forever.
If you commit a Major Atrocity, you will be expelled from the Planetary Council and all factions will pronounce Vendetta against you.
Simple atrocities commmitted between factions of different species (i.e., the Progenitors and humans) do not invoke the wrath of other faction leaders.