Japanese Title: 使徒、侵入 (Shito, Shinnyuu) (Angel Invasion)
English Sub-Title: Lilliputian Hitcher
Airdate: December 27, 1995
Ritsuko Akagi completes maintenance diagnostics on the MAGI Super-Computer System, just in time for the scheduled Evangelion harmonics experiments. Shinji Ikari, Asuka Langley Sohryu, and Rei Ayanami are inside special simulation Entry Plugs, which are then inserted into Evangelion simulation bodies. The mock Evangelion Units, appearing as half-finished bodies without heads or legs, are used strictly for data collection and analysis.
As the experiment progresses, the NERV Command Center detects an abnormality on one of the recently installed protein walls. After analysis comes back inconclusive, it is decided that it is most likely corrosion due to sub-standard installation. NERV Vice Commander Kouzou Fuyutsuki orders it to be fixed as soon as possible.
Ritsuko Akagi is notified of the corrosion, which is incidentally just above the floor where she is conducting her experiment. Noting that they cannot abort complex experiments due to minor technical glitches, she orders the experiment ahead.
Suddenly the corrosion begins to spread at an alarming rate, contaminating the experiment. Within moments, Rei lets out a scream as her simulation body is infected by the corrosion. As her infected arm reaches towards the control room, it is severed from the simulation body, and the Entry Plugs are immediately ejected. An AT Field is soon detected, and the infection is identified as Ireul, the Eleventh Angel.
NERV Headquarters begins to lockdown the facility in their efforts to isolate and contain the Angel. NERV Commander Gendo Ikari however cancels the alert, ordering that the Human Instrumentality Committee be contacted and told that there was an error in the alert system. As the infection continues to spread, Gendo orders the immediate evacuation of the inactive Evangelion Units, giving priority to Evangelion Unit-01.
After a failed attempt to contain the Angel using ozone, an intruder is detected inside the computer system. Moments later a trace is complete, showing the hacker to be the Angel itself.
As the Command Center struggles to contain the invasion, Ireul begins to hack into the MAGI Super-Computer System. Melchior-1 is quickly reprogrammed by the Angel, submitting a self-destruct order. Fortunately, the order is rejected and overruled by Balthasar-2 and Casper-3. Having failed, the Angel proceeds to hack into Balthasar-2.
With the MAGI Super-Computer System nearly overtaken, Ritsuko Akagi suddenly orders to change the logic mode and alter the synchronization code to every fifteen seconds. Although this does not stop the attack, it slows it down dramatically, buying the Command Center about two hours to formulate a plan.
Misato Katsuragi explains that the only way to destroy an organism that evolves at such a pace is to destroy its host. She therefore proposes the physical destruction of the MAGI Super-Computer System. Ritsuko Akagi is quick to counter that this is the responsibility of her department, and that to destroy the MAGI is to destroy NERV Headquarters itself.
Ritsuko suggests that as long as the Angel continues to evolve, they have a chance. She proposes to set up the MAGI to be absorbed by the Angel, and guide it to an evolutionary dead end (self-destruction). However in order to have such a program ready in time, Ritsuko must physically enter and reprogram Casper-3, where to her surprise, she finds a tunnel filled with developer notes left by her mother.
As Ritsuko works on reprogramming Casper-3, Misato asks her about the MAGI. Ritsuko explains that the system was developed by her mother using a personality transplant operating system, and it was her personality in the system. When Misato asks if that is why she wants to protect the MAGI, Ritsuko answers that she does not think so, considering that she never liked her mother. She tells herself that her decision was that of a scientist.
Ritsuko gains access to Casper-3 just as Balthasar-2 is overtaken. Soon Casper-3 comes under attack, and the facility's self-destruct is activated. Ritsuko races against the clock to install the necessary programming before Casper-3 is lost. With only one second left, Ritsuko's program is initiated, halting the countdown. The MAGI Super-Computer System recovers, immediately cancelling the self-destruct. Ireul's biological circuits begin to break down as the Angel seemingly reaches an evolutionary dead end.
In the meantime, Shinji, Asuka, and Rei are floating inside their simulation Entry Plugs on the surface of the Geo Front. Still naked from Ritsuko's experiment, the three await to be rescued.
As Misato Katsuragi brings Ritsuko coffee (or paint thinner as she describes it), Ritsuko explains that the three MAGI systems were designed after the three aspects of her mother's persona, her as a woman, a scientist, and a mother. These three aspects are struggling for dominance, and that her mother intentionally implanted the dilemmas of the human experience into the system. Ritsuko confesses that she did not understand her as a mother, respected her as scientist, but hated her as a woman. Ironically, Casper-3 is that aspect of her mother's persona.