The Deleted follows members of a cult in Northern Washington who escaped to Los Angeles and go off the grid. When escapees begin disappearing, they're driven to find one another for protection as nefarious cult leaders hunt them down.
Logan finally contacts Ryder, who confronts him about his abandonment of the escapees. Garrett agrees to assist the Institute and pays a visit to Agatha.
With Mason, Garrett, and Logan missing, Agatha grows increasingly paranoid. Breeda seduces a stranger while following a lead.
Agatha's injuries convince Ryder to relocate. Breeda pays Kennedy another visit and ignores Parker's orders to avoid violence.
Logan tells Parker the truth about what happened at the Institute. Ryder takes matters into his own hands.
The leaders of a mysterious cult arrive in Los Angeles to track down the young men and women who escaped.
Logan is violently evicted as tension escalates among the escapees. Garrett visits a friend in need, and another kidnapping occurs.
After Agatha's disappearance, Ryder encounters the Genesis patient. Logan draws closer to the edge of oblivion.
Video diaries from six months earlier reveal the Institute's experiments with the escapees.