Misato is summoned before the UN committee where she is questioned directly on the events that took place during the last mission and whether she believes the pilot of Unit 01 to be fit to resume active duty. Meanwhile, whilst this is all happening within NERV HQ, Toji makes his daily visit to the hospital to check on the progress of his little sister who was injured during the first battle of Tokyo-3.

All hell breaks out at NERV as they learn that the second branch of NERV in the Nevada desert, America, has just vanished from the face of the Earth along with EVA-04, its newly installed experimental S2 engine and thousands of people. Ritsuko believes the disappearances to be related to the manor in which Unit 01 was engulfed by the twelfth Angel, but without any clues as to what caused the disaster, Ritsuko can only speculate at best what happened. Therefore the US government, unwilling to risk NERV's first branch, force EVA-03 onto the third branch of NERV in Tokyo-3, of course the decision to unload all their problems on to branch three is proving very unpopular with Misato.

With the arrival of Unit 03, NERV find themselves with the prospect of having to activate the Eva for the first time. Ritsuko believes the use of the prototype dummy plug autopilot system would be ill advised, and so a fourth Eva pilot is found, but the speed at which the fourth child is found causes Misato to become extremely suspicious. Unable to get any answers from Ritsuko, Misato decides to seek help from Kaji who later reveals to her that the Marduk institute doesn't even exist, and that NERV its self is responsible for Eva pilot selection.

Knowing the fourth child to be another of Shinji's classmates, Toji Suzuhara, makes Misato's task of informing Shinji of the new pilot very difficult indeed. Shinji's been through some tough stages recently, even depression, therefore Misato is understandably weary of exposing him to any more stress, but with Shinji bound to find out sooner as opposed to later, Misato figures she'll have no choice but to tell him regardless. Asuka's also not looking forward to the arrival of the new pilot, the last thing she needs is more competition.

Genesis 0:9/Episode 18 - The Judgement Of Life

Misato, who reveals the rumours to be true, finally confirms Shinji's suspicions concerning the second branch of NERV and EVA-04 along with its experimental S2 engine. Apparently Unit 03's scheduled for arrival at the Matsushiro test facility today and so Misato's off to over see the initial activation of the Eva, however, she assures Shinji that all will be ok, and that she'll be back in the afternoon. Again she can't bring herself to reveal the identity of the fourth child who will pilot the Eva during its first activation test.

Toji reluctantly accepts the responsibility of becoming the pilot for Unit 03, however, he only does so on the condition that his little sister be transferred to one of NERV's private hospitals where she'll receive specialist care and treatment. Although Toji attends school as usual, he spends most of the day out of class contemplating what he's let himself in for, his new behaviour also arouses suspicion in both Shinji and Kensuke who's desperate to be chosen as a future Eva pilot.

Unit 03 finally arrives at Matsushiro and the test gets immediately under way despite Misato's lack of enthusiasm, but what would normally be a routine test by now, turns into a nightmarish disaster when the thirteenth Angel, Bardiel, is detected within the Eva's body! With Unit 03 out of control and running amok Commander Ikari classifies the Eva as the thirteenth Angel and orders its destruction. Asuka takes a severe beating failing to stop the Eva, Rei also aborts the mission when the Angel merges with Unit 00's arm forcing NERV to cut it off, however, Shinji just can't bring himself to attack the Eva, he doesn't want to risk harming the pilot whoever he or she may be.

With Units 00 and 02 out of action and Shinji at the mercy of the Angel, Commander Ikari orders the activation of Unit 01's dummy plug. Despite having carried out no prior testing of the dummy plug system and vigorous objections from Maya, the order to initiate the system is carried out. With the dummy plug active Shinji can only scream and look on in horror as he is unable to prevent Unit 01 from literally ripping Unit 03 apart.