Non-brainwashed
Murder Monkeys - Work with Rosie and the Toulon puppets to solve the problem
Agatha and Jezebel - Tries to find survivors (especially kids who were not brainwashed and are still alive)
Edith - Tries to soothe the surviving children by playing her violin in the shelter
Dread Duckies - Sacrificed their sewers as shelters for those who survived
Clown Gremlins - Sent an army of themselves to attack the Monokuma clones
Reaper Nurses - Takes care of sick or injured survivors and kept them hidden in a basement at a local hospital that was abandoned
Remnants of Despair (mainly most of the JJG members)
Lucky - Leader of the Remnants of Despair and Junko's right hand man
Penny - Serves for Lucky as she uses her eggs that were filled with acid against the Future Foundation not to mention she was the second victim to be brainwashed
Hangry - Kills living families, cooks them and eats them in front of the survivors
Cobalt - Injected so many people full of Psycho and made other drugs that potentially killed them along with making Penny's eggs full of dangerous acid
Waverly - Uses her motorbike to run people over and works with Hangry, Penny and Cobalt
Matryoshka - Rams people into walls giving them concussions and potentially smashing their skulls open
Daley - Cuts his ears off and goes on a murder spree to "silence" everyone and the first victim to be brainwashed
Destiny - Died in the Ultimate Punishment which led to Matryoshka falling into despair the most and Echo trying to find a cure
Future Foundation
Echo - Foresaw the Neo-World Program and was able to place her brainwashed friends in the pods
Mama Bear - Stuck in one of the Killing Games in the foundation but was able to find a loophole
Trigger Teddies - Personal body guards for Mama Bear
Ursalina - Pretends to work with the Warriors of Hope but is secretly a spy for the Future Foundation to get information out of them
Gold Watchers - Works with the Future Foundation as body guards