Five Nights at Sonic's VI welcomes you to a brand new chapter in the series that finally uncovers the mysteries of SHPP itself. Following the events of Rockclones, the discovery of SHPP HQ has hit the news, causing people to take interest and dare venture into the building that sparked the rise of the clones. However, none who entered came back, and Clone Sonic vows to get to the bottom of this through a series of night expeditions. It doesn't take long until he learns that this abandoned headquarters has been transformed. In fact, it has become the territory of the forgotten projects who survived...

At SHPP HQ, Clone Sonic will meet the Pseudos, the forgotten projects that survived. The Pseudos are clones and animatronics left behind due to being defective, but as time passed and the company ceased to exist, these entities began to transform into strange monsters who will ferociously defend what has become their territory.