Prior to the events of Digital Devil Saga: Avatar Tuner, Jenna Angel managed to gain limited control over the Junkyard. This allows her to spread the Atma virus she had been developing for 5 years, infecting every one of the Junkyard's inhabitants for the dual purpose of testing it and using them to retrieve Sera.
Jenna Angel initially conceals her true identity under the avatar of Angel, though Varin Omega sees through it after regaining his memories upon awakening to his identity as Colonel Beck and Gale recognizes her on sight after awakening to his own personality and memories. She is idle during most of the conflict in the Junkyard as she awaits for the victorious tribe to bring Sera to her, only appearing to decree the new commandment of the Karma Temple and to lend Varin her Hunger Wave ability after gaining more control over the Junkyard.
After the Embryon win the war in the Junkyard, Sera regains her memories and climbs the Temple on her own accord, intending to confront Angel on her own. Angel appears there personally, intending to take Sera back with her for her own purposes. She reveals that she has gained full access to the Junkyard, using it to delete Sera's Rakshasa and begin deleting the Junkyard. The Embryon reach the top of the Temple themselves and engage Angel in battle, despite Sera's commands, which results in the destruction of Angel's control sphere. This dooms the Junkyard to destruction, forcing them to escape.