Shintaro Kisaragi is a shut-in isolated for 2 years, living his life normally until he met a virtual girl named Ene - who seemingly only exists in cyberspace - who appeared in his computer screen when someone anonymously sent him an e-mail a year ago.
Ene messes with Shintaro's computer, which causes the computer to break and forces Shintaro to enter the outside world for first time in two years. He heads to the department store, where a group of criminals break in and hold the people inside hostage for ransom.
Here he comes in contact with a group of teenagers calling themselves the "Mekakushi Dan" (or the "Blindfold Gang"), who stop the robbery with their powers and coerce Shintaro into joining their group.
This anime is part of an overall mixed-media project known as the "Kagerou Project".