Within City 31, there are three main enemy factions, each with their own agenda and beliefs. These factions are Gray Phoenix, The Progeny, and Sacred Coil. In addition, all three are assisted by a fourth faction, Shrike, who often serve as backup.
- Main article: Gray Phoenix (XCOM: Chimera Squad)
Gray Phoenix is a group of alien scavengers. While they are primarily made up of Mutons, Gray Phoenix also makes use of Sectoids and various species of Vipers. Gray Phoenix kidnaps highly skilled alien engineers so that they can repair a damaged alien vessel from the invasion, and use it to escape Earth - not back to their former masters, but to a place they can call home. They are led by two individuals: Former Muton EngineersCustodian Xel and Crew Chief Yarvo. Yarvo is in command of their ground teams while Xel oversees all technological projects. However, there is no record of either in any Post-War prisons.
- Main article: The Progeny (XCOM: Chimera Squad)
The Progeny is an all Human network of psionics. They believe in a future for City 31 that is completely psionic and will do whatever they can to further this agenda. The Progeny strengthen their numbers by abducting Hybrids and indoctrinating them into subservient thralls. The Progeny's main goal is to induce a psionic evolution on the inhabitants of City 31. They are led by Violet, a product of ADVENT experimentation, she induces psionic capabilities upon The Progeny's membership.
- Main article: Sacred Coil (XCOM: Chimera Squad)
Sacred Coil is an underground religious movement founded by ex-ADVENT officers and preach salvation for the other species who were once a part of the Elders' invasion of Earth. Sacred Coil's main source of propaganda is the claim that they have a cure for The Fade, a disease that only affects hybrids. Sacred Coil's endgame is to repair a Psionic Network gateway in their underground cathedral to try and gain a glimpse of the Elder's wisdom. They are led by Bellus Mar, a former ADVENT commander never caught after the war. Bellus Mar is the genetic template for Cherub.
- Main article: Shrike (XCOM: Chimera Squad)
A group of human ex-Resistance and XCOM personnel disgusted with the more pacifist route to reunification advocated by XCOM. While they are only fought directly in the final two missions, they often show up as mercenaries in the employ of other factions. Their leader goes by the call sign Sovereign, who believes that the Elders will return and that in order to be ready XCOM must "tear the weakness from their hearts."