After your first mission you choose the target of your investigation. This guide on What Faction To Choose In XCOM: Chimera Squad breaks down the different faction choices you can make and explains the events that follow, depending on the decision you make.
The introduction mission in XCOM: Chimera Squad is a tutorial that introduces the games various mechanics, new and old. You’re introduced to the brand new Breach feature alongside other new mechanics such as knocking enemies out instead of killing them. Once you have completed this mission and returned to base, you’re given a choice on what faction you want to investigate.
What Faction To Choose In XCOM: Chimera Squad
There are three choices to make here. Below is the break-down of each faction as displayed in the game.
A loose network of human psions. Their vision for City 31’s future is entirely psionic – whether the city wants it or not
An organization of alien scavengers. They have quietly amassed the kind of weaponry Reclamation is mandated to recover
An underground religion movement for hybrids. They preach salvation, but only to those who once fought XCOM.
This is not a right and wrong choice scenario. Each different faction presents a different path of progress through the story. Once an investigation has been resolved, it is possible to launch another investigation against another target faction. Each investigation is the same in terms of the design. Groundwork, Operations, and Takedown. Each stage for each faction presents different missions and challenges but the general design direction remains the same.
Each faction belongs to one of the races inhabiting City 31. The Progeny are the Humans, the Gray Phoenix the Aliens, and Sacred Coil, Hybrids. Each faction also corresponds loosely to characters in the Chimera Squad, having at least one Alien, Human and Hybrid within the group. Certain story archs involved in each faction do involve the corresponding characters from the Chimera Squad but again, every potential avenue can eventually be explored.
from GamersHeroes http://www.gamersheroes.com/game-guides/what-faction-to-choose-in-xcom-chimera-squad/