Having picked up their laundry, Ritsuko and Maya Ibuki, one NERV's scientists, unintentionally meet up with Commander Kouzou Fuyutsuki on their way home via the Tokyo-3 loop line. Fuyutsuki's on important business due to represent Commander Ikari in a city council meeting. Ritsuko makes small talk by casually mentioning the city's up coming election, but soon learns from the Commander that the election is effectively irrelevant. Apparently the MAGI, the same three super computers that NERV use, are now responsible for most of the city's decision making.

Without any warning all power to the geo front and NERV HQ is suddenly cut and the three backup power supply systems fail to respond leaving NERV crippled. For all three systems to fail is unheard of and a near impossibility implying one thing; they didn't go on their own accord. This leaves NERV defenceless and vulnerable to an Angel attack, the situation is even worse for Misato who's trapped inside an elevator along with Kaji as her only source of company. Asuka, Rei and Shinji, however, are stranded out side NERV HQ struggling to gain access to the complex, fortunately Asuka's leadership skills, based heavily on Rei's guidance, sees the party headed in the right direction.

The ninth Angel, Matariel, is headed towards Tokyo-3. With NERV unaware of the Angel's presence and all communications with them lost, the JASDF fly directly over the city informing the inhabitants of the imminent Angel attack. NERV eventually learn of the situation and so Commander Ikari has Units 00, now having finished being upgraded, 01 and 02 prepared for manual launch, the pilots also finally arrive in their usual argumentative manor.

All three Units are launched and engage the Angel, which is positioned directly above them and NERV HQ. It's attacking using some kind of extremely corrosive acid, which is melting through the geo front's defensive armour and also that of the Evas'.

With the Angel's strange offensive capabilities, an all out frontal assault is out of the question, however, Asuka has a half descent plan of her own for a change, one which might actually work.

Genesis 0:6/Episode 12 - The Value Of A Miracle Is

Misato has a flashback to 2000 AD, 15 years ago, and the exact point in time when the second impact struck Earth. She recalls how her fatally injured father hurriedly secured her within an escape pod before contact with the impact's shock wave, and then looking out from sea back on the horrific devastation caused by the first Angel.

The latest harmonics test reveals Shinji to be somewhat of a talented Eva pilot, his harmonics and synchronisation ratios are rapidly catching up with Asuka's much to her disgust, however, Misato knows that this isn't really what Shinji wants. Later whilst being driven home after the test, Shinji congratulates Misato on her promotion to the rank of Major, but it would seem that Misato isn't to thrilled about the idea. Nevertheless the celebrations go ahead, as ordered by Kensuke, and even Kaji manages to turn up, although accompanied by Ritsuko.

Whilst Commanders Ikari and Fuyutsuki attend business in Antarctica, home now to the true dead sea, Misato's left in charge of NERV for the very first time. Unfortunately though, her debut as head of NERV's operations isn't going to be an easy one as the tenth Angel, Sahaqiel, shows up, this time in space directly above the Indian ocean. The Angel's effectively a huge living bomb and is targeting NERV HQ by dropping small fragments of its self on to the Earth whilst steadily correcting its error ratio. Once the Angel has acquired its target, NERV suspect that the Angel its self will descend on to NERV HQ effectively wiping it off the map, therefore Misato is now faced with the near impossible task of preventing such an event from taking place.

By expanding their AT fields, Misato intends for all three Evas to catch the Angel before it strikes the ground. To describe the plan as futile would be an understatement, but with the only other option being to sit back and watch the third branch of NERV being destroyed, Misato is willing to risk all three Evas. Prior to the operation, Misato confides in Shinji revealing her true feelings towards her father and her reasons for joining NERV, this in turn reveals her hatred towards the Angels and why she's willing to risk sacrificing the Evas.