After securing the Rainbow Factory complex, rebel forces, with royal Canterlot support, swooped into Cloudsdale and deposed the ruling government. Resistance was minimal, as most officials involved with the Factory had already committed suicide rather than face punishment for their many crimes against ponykind. All officials found not to have any knowledge of the Factory were returned to their jobs to aid the rebels in rebuilding Cloudsdale’s government and economy (news of the Factory’s existence had wiped out the tourist industry), and would eventually reform the Constitution of Cloudsdale to add more transparency to both government and corporate practices, ensuring something as monstrous as the Rainbow Factory would never happen again.

Every one of the officials found to have been supporting or covering up the Factory’s existence were found guilty of high treason and given sentences varying from life imprisonment to banishment in the wastelands. Most of the Factory’s workforce and management are now in programs meant to wipe out the Owner’s brainwashing techniques, while all those found to be clear of brainwashing are now serving jail time.

Rainbow Dash fell into a self-destructive life of drugs and isolation a few weeks after the rebels overran Cloudsdale, only leaving her house after her friends staged an intervention and convinced her to enter therapy to deal with the massive trauma of the things she’d seen and done while undercover in the Factory. After months of intensive therapy, she was deemed mentally fit and returned to her Cloudsdale home, where her friends were waiting for her. She still attends weekly counseling sessions with professional therapists provided by Celestia herself, and there are still nights where she wakes up screaming about bloody hooves in the dark, but her friends are always there to help her when she falls.

Scootaloo’s training with the rebels would pay off when she tried out for the Wonderbolts, making it into their ranks and rising to become team leader. She still stays close to Cloudsdale and checks in on Rainbow Dash every time she has the chance. In return, Rainbow hasn’t missed a single one of her former student’s shows, and has even been asked to perform with her on numerous occasions. The shows where Rainbow Dash and Scootaloo perform together are widely considered to be the best and most spectacular.

Cloudsdale has healed from the wounds left by the Factory, but the toll lives on in the hearts of those who lost loved ones. The memories still sting for many, but most have learned to move on and cope, to live their lives as those lost souls would have wanted them to live. That’s all that can be asked of them.