It's been twenty two days now since the pilot of the Eva prototype, EVA-00, mysteriously lost control of her Eva during her first attempt to synchronise with the Unit. Twenty two days since Rei was seriously injured, despite having been rescued by commander Ikari who opened the super heated hatch on Rei's entry plug with his bare hands, a courageous action which left his hands permanently scared. Now Rei is preparing herself to re-undergo the synchronisation process with Unit 00.

Ritsuko heads up the salvage operation for the fourth Angel which, due to the manner in which the Angel was disabled, NERV have been fortunate enough to obtain as it's a near perfect specimen for which to study. Analysis of the Angel reveals its structural composition, although being composed of different matter, to be almost identical to that of humans. Whilst Ritsuko and Misato analyse the data, Shinji notices the scaring on his father's hands whilst he examines the Angel's corpse. Misato arrived at NERV after the incident with the prototype Eva, however, Ritsuko knows all to well the events in question and agrees to fill Shinji and Misato in on the details.

Later that evening, having agreed to join Misato and Shinji for dinner, Ritsuko gives Shinji Rei's new security card to pass on. Apparently Ritsuko's forgotten to pass on the card in person, at least that's the story, and so Shinji gets the job, along with an excuse to go over to Rei's place. The following day Shinji takes the card over to Rei's, however, it doesn't quite go as planed when the third child manages to elegantly end up on top of a naked Rei on her bedroom floor. Matter aside though, the two of them proceed together to NERV HQ where Shinji discovers that Rei appears to have the kind of relationship with his father that he has always longed for.

The fifth Angel, Ramiel, arrives in Tokyo-3. As the successful synchronisation between Rei and Unit 00 has only just been completed, it's decided that Rei is still unfit to fight and so Shinji in Unit 01 is launched. With little or no data on the new Angel, however, this soon proves to be a huge mistake.

Genesis 0:3/Episode 06 - Showdown In Tokyo-3

The fifth Angel fires upon Unit 01 immediately after having surfaced. The attack is made using an extremely high powered energy discharge which, due to Misato's quick thinking to retrieve the Eva, manages to only burn through Unit 01's front defensive armour melting it down to the third layer. Given three more seconds though, would have resulted in the Angel shooting right through the Eva, fortunately, however, the rest of Unit 01 remains undamaged and Shinji looks set for a quick recovery.

To learn more about the new Angel's offensive and defensive capabilities, Misato has UN forces move an inflatable to scale sized Unit 01 decoy into the Angel's estimated firing range. She also has the Angel attacked with a German type 12 self-propelled mortar, both of which are vaporised instantly. The results show the Angel to be equipped with a large firing radius and an exceptional AT field. It's also learned that the Angel is positioned directly above the geo front, home to NERV HQ, and is boring towards the instillation intent on attacking NERV directly.

Due to the Angel's remarkable offensive and defensive capabilities, Misato comes up with a plan to attack the Angel with a sniper. Commander Ikari approves the plan and Misato is put in charge of the operation. As NERV's positron rifle is unable to handle the massive output required to penetrate the Angel's AT field, Misato requisitions the SSDF's new prototype self-propelled positron cannon, meanwhile Ritsuko comes up with a novel form of temporary shielding against the Angel's fire.

Besides the poor estimated success rate for the mission, there is also another drawback to Misato's plan. With so much electricity being required to power the positron cannon, at half past eleven that night the whole of Japan is scheduled for a large scale power blackout so that NERV can get enough power to the cannon.

With Shinji now ready as the sniper and Rei providing the defensive backup, the plan is set and put into operation, but in a war against the Angels, even a predicted eight point seven percent success rate isn't guaranteed.