Atrocities comprise a set of particularly heinous acts forbidden under the Unity mission's U.N. Charter, such as using Nerve Gas Pods, Planet Busters, obliterating bases, and Nerve Stapling drones. Committing them while the U.N. Charter is in place will cause other factions to impose sanctions which prevent commerce for a number of years (the length of sanctions depends on how many atrocities a player has previously committed). The length of sanction time left can be seen on the energy screen (F3).
All factions will pronounce Vendetta on a faction which commits a Major Atrocity or a large number of Simple Atrocities, they will be expelled from the Planetary Council, and will cause increased eco-damage. Victims of atrocities do not tend to forgive those who committed them.
Simple atrocities committed between factions of different species (i.e., the Progenitors and humans) do not invoke the wrath of other faction leaders.
For more information see Atrocities (Advanced).