Episode:13

"An Angel's Invasion" is the thirteenth episode of Neon Genesis Evangelion.

Overview
The pilots are undergoing a synchronization test directed by Ritsuko deep within NERV Headquarters when a new Angel, Ireul, appears within the base itself, being initially mistaken for corrosion. This Angel is actually a collection of millions of microscopic organisms, which interact to create a living biological computer circuit. Iruel infects NERV's computer network, and then infiltrates two of the three Magi supercomputers that control the base before Ritsuko is able to set up a firewall to slow its advance. Iruel is trying to trigger the NERV base's self-destruct, which requires a unanimous vote by all three supercomputers. Although Ritsuko's firewall slowed the advance of Iruel's infiltration, it is gradually taking over the last supercomputer. Ritsuko comes up with a scheme to use the Angel's rapid adaptive ability against it and force it to evolve in to a benign state, but must race to implement it before the Angel gains control.

Synopsis
Episode 13 begins with Ritsuko Akagi completing a routine maintenance test of the Magi supercomputer system, followed soon by an autopilot test for the three Eva pilots. The pilots are supposed to enter simulation bodies without their plug suits and after a thorough disinfection.

The pilots enter the "simulation plugs", the entry plugs for the simulation bodies kept inside the Pribnow Box , while the Magi monitor the data coming off their bodies. While the test proceeds smoothly, Aoba shows Fuyutsuki what look like stains on construction brought in three days previously. Hyuga thinks they are corrosion from trapped air bubbles, and Fuyutsuki reminds them to fix the problem by the next day.

Maya informs Ritsuko of the corrosion in the protein wall above, but since it does not pose any problems to the test for the moment, Ritsuko decides to go ahead, saying that they can't abort the test due to minor technical issues. The simulation plugs are then connected to their Evas via their simulation bodies, contact being first established with Unit-00. Immediately afterwards, a contamination alert sounds as the corrosion begins to spread explosively. The experiment is aborted and several water pipes sealed to prevent the spread, but to no avail.

Without warning, Rei screams and her simulation body starts moving and trying to break free of its restraints. It raises a hand towards the control booth, but the arm is severed by a blasting bolt and the pilots are ejected at once. The mass of corrosion is fired upon with lasers, but to everyone's shock and horror, it deploys an A.T. Field, revealing itself to be the eleventh angel, Ireul. Immediate panic ensues in the command facility, and Central Dogma is closed off at once and all personnel evacuate the Pribnow Box. Gendo cancels the alarm, and orders that the committee and the Japanese government be informed of an error in the alarm system. He then orders the Evas to be launched pilotless to avoid the risk of infection, giving Unit-01 priority

Meanwhile, Ritsuko and Misato attempt to fight the angel without the Evas. An attempt to destroy the Angel with an excess of oxygen fails as the angel evolves, soon turning into a system of electronic circuits that attacks NERV's computer systems, reprogramming the Magi Melchior and attempting to initiate self-destruct for the facility. Unable to get clearance from the other Magi, it starts hacking into Balthasar as well. However, a temporary firewall is set up that prevents the Angel from hacking any further for the time being.

Ritsuko explains the nature of this new angel: a colony of microscopic entities working together to evolve and form intelligent circuits, and details a plan to counter-hack the Angel and program it to reach an evolutionary dead end, where it will have no choice but to die. She opens an entrance into the physical structure of the surviving Magi Casper, and begins work with notes left by her mother.

Ireul finally breaks through the firewall and completes infecting Balthasar, and with one second to go before Casper is defeated, the counter-hacking program is installed. The Magi are promptly restored to their normal status, and Ireul dies out. Ritsuko talks to Misato about the Magi and her mother's personality, and the pilots are left wondering what happened.

Analysis

 * Misato's drive to destroy Angels and sense of intuition cause her to suggest the physical destruction of the Magi so that the Angel has no growth medium. This time, it is Ritsuko's logic and clear thinking that win out.
 * Misato thinks that the same "Personality transplant" operating systems used by seventh-generation computers to think for themselves are also in the Evangelions. Misato is rarely in the know, and whether or not she is right or wrong on this issue is an open question: Ritsuko does not answer her, and the question is never brought up again.