Reclamation has identified three major criminal organizations active in City 31. All are suspected to have the means and motives to have Mayor Nightingale assassinated, and it is up to Chimera Squad to stop their plans and discover the truth behind the mayor's murder.
The Progeny are a network of human psionics, backed up by brainwashed alien and hybrid Thralls who provide muscle. They envision a wholly psionic future for City 31, one that they will force upon it if necessary. To fund their schemes, they mind-control citizens into giving up their valuables and then erase their memories of the experience to cover their tracks.
Flashbangs and Burning are highly effective to disable their psionic abilities, but their psionics still carry pistols, so don't expect them to be helpless after a Flash Bomb- especially since they are immune to Weapon Disable.
- Thrall: A mind-controlled hybrid with a shotgun, used solely as cannon fodder and as targets for Subservience.
- Acolyte: The basic Progeny psionic soldier. In addition to their pistols, they can use Soulfire to inflict armor-ignoring damage and Psionic Suplex to lift an agent out of cover, slamming them to the ground on the next turn to inflict damage. They resist most psionic effects.
- Brute: A mind-controlled Muton that can stun enemies in melee. After moving or shooting, it can enter Melee Stance to attack nearby enemies as a free action. When damaged, it triggers Bloodlust to move towards the attacker.
- Resonant: A mind-controlled Sectoid with an assault rifle and supportive psionic abilities. Soul Siphon causes the Resonant to damage itself in order to heal a nearby ally, and and Psi Domain enhances the attack power of all Progeny psionic attacks. If killed, they release a psionic burst that makes nearby agents panic.
- Codex: Similar to its XCOM2 appearance, retaining its ability to teleport and/or clone itself when damaged along with Psionic Bomb. Stunning, disorientation, and Torque's Bind can all prevent it from using its abilities.
- Archon: Similar to its XCOM2 appearance, though it should be noted that Burnout (formerly Blazing Pinions) now works indoors. Burnout targets the position of three of your agents, but can be cancelled by stunning the Archon before the next turn begins. A damaged Archon will use Battle Frenzy as a free action to move and potentially perform a melee attack.
- Sorcerer: Elite human psionics that can teleport and are immune to all mental effects (including disorientation and stuns). They can use Tyranny to grant an ally an extra action, and their Subservience ability transfers all damage that the Sorcerer takes to a chosen ally. Offensively, they can damage multiple agents at once with Force Lance and heal themselves with Writhe.
- Violet: The Progeny's leader, a byproduct of a forgotten ADVENT experiment gone horribly wrong that gained the ability to awaken psionic powers in others but was driven insane in the process. She can use all of the Sorcerer's abilities, and is also immune to Bind and Tongue Pull. She will automatically teleport when hit.
Gray Phoenix are a medley of alien scavengers, fielding primarily Mutons backed up by Viper skirmishers and Sectoids for psionic support. While their goals are unclear, they have recently been stockpiling large quantities of Elerium and contraband weaponry to a degree that puts them under Reclamation's jurisdiction.
They are dangerous in close quarters, especially when deploying Faceless and Berserkers.
- Legionnaire: A basic Muton soldier with a shotgun. Their Demolition ability deals no damage but is guaranteed to destroy cover.
- Adder: A Viper skirmisher. It gains a significant bonus to Dodge and Mobility as a free action after moving or attacking, and has a poisonous melee attack.
- Python: A Viper that specializes in the use of Tongue Pull and Bind.
- Paladin: A Sectoid with supportive psionic abilities. It can mind link with allies to grant them bonuses to Aim and HP, but killing the Paladin will also kill whoever it has mind linked with.
- Dominator: An offensively focused Sectoid psionicist that can stun or mind control agents.
- Faceless: The Faceless no longer disguise themselves, but retain their HP regeneration and sweeping melee strikes.
- Berserker: Similar to its XCOM2 appearance and can now disorient with its melee attacks in addition to stunning targets or knocking them unconscious. May go Berserk if damaged, causing them to attack the nearest available target even if that target is an ally.
- Sectopod: Virtually identical to its XCOM2 appearance.
- Praetorian: An elite Muton soldier with heavy armor who can boost its allies' armor once per battle; its armor level also gets passively buffed each time it is attacked (by +1 per stack until the end of the turn). Its melee attacks can stun or disorient, and it can challenge an agent to a Duel to guarantee its attacks will never miss that agent. However, the challenged agent will also be guaranteed to hit the Praetorian.
- Crew Chief Yarvo: Co-leader of Gray Phoenix, responsible for its ground operations. An enhanced Praetorian.
Sacred Coil is an Elder-worshipping cult, founded by former high-ranking ADVENT officers. By taking advantage of The Fade, an incurable wasting disease that only affects hybrids, they play to the bitterness and resentment of those who benefitted from ADVENT's rule and claim that those who fight X-COM will receive salvation and a cure for the disease.
Sacred Coil fields hybrid soldiers of varying sorts with a great deal of mechanized support. They notably lack psionic support, though they compensate by fielding Chryssalids and Andromedons.
- Commando: The basic Sacred Coil soldier, equipped with a smoke grenade it will use to protect itself.
- Purifier: A flamethrower-equipped soldier that will try to burn agents and terrain. Once per mission, it can throw an incendiary bomb that sets a 3x3 area ablaze. It is immune to fire, acid, poison, and all grenade effects.
- Android: An android soldier, similar to the ones that Chimera Squad can deploy. It can self-destruct at will to deal damage in a 2-square radius, and will also do so if killed.
- Guardian: A soldier armed with a pistol and shield, similar to an ADVENT Shieldbearer. They can provide a shield to nearby allies that acts like a pool of temporary HP; killing the Guardian will not remove the shields it has already granted.
- Turret: Similar to the ADVENT Turret, but can only shoot once per turn. However, it can use Holo Targeting to buff its allies' Aim and can use Overwatch.
- Chryssalid: The flooring and pavement in City 31 is too tough for Chryssalids to burrow through, but they are otherwise similar to how they behaved in XCOM2. They will prioritize attacking civilians to create cocoons, which will spawn weaker Neonate Chryssalids until destroyed.
- MEC: Similar to its XCOM2 appearance. In addition to Micro Missiles, MECs can use Pin Down to delay an agent's actions on the Timeline.
- Andromedon: Unchanged from its XCOM2 version. Notably, Axiom's melee attacks can knock it unconscious, preventing the suit from reactivating.
- Ronin: A fast hybrid soldier specialized in melee combat, somewhat like an ADVENT Stun Lancer. Tempo Surge grants it two bonus actions, and Lightning Reflexes protects it from Overwatch attacks. Its melee strikes have a chance to rupture, root, or disable weapons, and if it hits Bend the Reed will allow it to make a free move action. Finally, it can use Melee Stance to gain free attacks against approaching agents.
- Gatekeeper: Unchanged from XCOM2.
A paramilitary organization composed mainly of ex-Resistance members and disgruntled former X-COM soldiers "upset that the war didn't end with the conquest of the stars", who split off from X-COM over their irreconcilable differences on how Earth's society should be rebuilt after ADVENT'S defeat.
While initially seeming to be just an ordinary mercenary force (and indeed they acted as peacekeepers for City 31 before Reclamation arrived), it is eventually revealed that they were responsible for the mayor's assassination and had been providing resources to the other three factions in the hope of provoking a crackdown from X-COM, forcing it to take the authoritarian stance that they believe is necessary to ensure that the Elders cannot reconquer Earth. The hypocrisy of establishing a regime that would in practice be indistinguishable from that of ADVENT is dismissed by them as their opponents "not knowing what is at stake".
Shrike's mercenaries are composed of all species, though later in the game they will also incorporate remnants of the three other factions; earlier on, they may sometimes appear as support units for other factions under the pretense of mercenary work. Their own units are heavily armored, and many have multiple special abilities.
- Trooper: A basic human soldier (albeit an armored one) armed with an assault rifle.
- Hitman: A pistol-wielding human soldier that can disable weapons with standard attacks and enters Overwatch after taking an action.
- Bruiser: A human soldier with a pistol and shield. It can activate Riot Guard, gaining +1 Armor for one turn, a half cover bonus even when flanked, and becoming themselves half cover for allies. In melee, it can use Shield Bash to try and knock an agent unconscious.
- Necromancer: A Sectoid armed with an Assault Rifle. It will raise dead or unconscious humanoid enemies as Psi Zombies when possible. If no corpses are present, it will instead generate two Spectral Zombies, which will run at agents and explode. Stunning or disorienting a Necromancer will eliminate Psi Zombies, but Spectral Zombies will not vanish until the Necromancer is killed.
- Cobra: An armored Viper with a SMG. It can use Poison Spit to poison agents within a 3x3 area, or Rooting Venom to inflict unavoidable damage while immobilizing the target.
- Bomber: An armored Muton with a shotgun that takes half damage from all explosive attacks. It can throw an armor-shredding plasma grenade once per battle and can counterattack if hit in melee.
- Sovereign: The commander of the Shrike cell operating in City 31 and the instigator of the city's troubles. In addition to the abilities of the Hitman, he can use Sustain to survive a fatal blow with 1 HP while going into stasis and cannot be affected by most negative conditions.