The Instrumentality Committee, the branch of SEELE responsible for NERV, appears after the battle against the Third Angel to berate Gendo Ikari for the damage suffered by Evangelion Units 00 and 01 and to the city. They consider the Eva’s and war against the angels as ‘pet projects’ compared to the Instrumentality Project. It is made of five men and led by Keel Lorenz.
Kaji reveals to Shinji that the organisation behind his father is a secret society called SEELE. He says that they have ruled the world for hundreds, or thousands, of years and paid for NERV's construction. They are in possession of the Dead Sea Scrolls which lay out the entire history of humankind – present and future.
Fuyutsuki believes that, in light of the Eva 04 incident, SEELE is looking back over the Dead Sea Scrolls to revise their predictions. The Committee is also mentioned as being alarmed at the loss of Unit 04 and the Nevada Branch.
After the battle with the Ninth Angel, the committee reconvenes to express its surprise that Eva 01 managed to obtain the S2 engine. They are also displeased with the serious damage to Eva 00 and Eva 02, as well as the NERV building itself. They awaken Tabris, Kaworu Nagisa, as their trump card against Gendo Ikari.
Seele appears as monoliths to interrogate Sub-Commander Fuyutsuki, with Keel appearing as SEELE 01. In flashbacks, Fuyutsuki reveals that the organisation was involved in an investigation into the causes of Second Impact and was most likely involved in the event. The group, through Keel Lorenz and Gendo Ikari, were responsible for a cover-up. After the Instrumentality Project was approved by Keel, the Committe for the Instrumentality of Man (Instrumentality Committee) was established to guide NERV's actions. By the time they interrogated Fuyutsuki, they have withdrawn from using the committee as a guiding tool.
They berate Ikari for his decision to use the Lance of Longinus in the battle against the Tenth Angel. They also discuss matters with Kaworu Nagisa, and remind him of the importance of reporting Ikari's actions to them earlier in future.
SEELE convenes after the destruction of EVA 00, believing that the recent losses of the Eva, Lance of Longinus and Tokyo-3 are ample reason to dismiss Ikari. They interrogate Ritsuko soon after and seem to try to manipulate her for their own ends.
The group meets with Kaworu to discuss NERV and particularly Gendo’s actions, entrusting to him their hope and using their trump card against NERV. After his refusal to initiate Third Impact SEELE considers that he might have betrayed them, but their Dead Sea Scrolls did not mention who the successor of life was meant to be. They determine that Gendo Ikari must be dealt with for his attempts to reject the destruction of Instrumentality and achieve his own version of the project.
SEELE is convened during the invasion of NERV, adjusting their plans when Eva 02 unexpectedly re-activates.