The Isolation Dimension, as its name implies, is an alternate dimension that isolates certain individuals from the normal world. Physically, the dimension looks no different from the norm, but the people in the dimension are completely cut off from those outside of it. In the Isolation Dimension, the Heartseeds can cause their phenomenons without worrying about any detrimental effects on the outside world. As described in Asu Random, it is similar to a laboratory for the Heartseeds to do experimentation. The people inside the Isolation Dimension can try to escape through the front door of the school, but everytime they take a step, they feel that they have moved but physically they are in the same spot they started. This is true for no matter what speed they attempt this, be it walking or running.
People outside of the area will not notice anything strange going on inside or notice that people are missing in the real world. Only individuals who have been directly involved with the phenomenons at some point will notice anything. Because their bodies were used by Heartseed and No.2 at some point, Hirata Ryouko, Gotou Ryuuzen, and Yaegashi Rina managed to notice that people were missing, and that the school was too quiet due to much of its student body having gone missing.
The dimension is exactly the same as reality but under the complete control of the Heartseeds. Yamaboshi High School is there but the principles of the dimension prevent the people trapped inside from leaving the school grounds. All communication devices such as cell phones and computers won't work. Water and electricity still run as normal, however. From what No.2 claims, the people inside don't need to eat, drink, or sleep. Injuries in this world are not physically there but the person will still feel pain. In this dimension, people are split into groups of 5, who are usually grouped by people who have good relations with each other or club members, and are forced to undergo different phenomenons that No.3 has planned. If an argument or conflict arises that may cause serious harm to another person, Forced Termination will be activated and the people involved will disappear and lose their memories of the people still in the Isolation Dimension.
- 118 students were trapped with the majority being second years with a ratio of 7 second years to 3 first years.